Planar area light source

ABSTRACT

A device, including: an end-emitting optical fiber including a first end and a second end; a light extraction plate including a light scattering structure; and a light diffuser film disposed above the light scattering structure. Also disclosed are systems including the device.

CROSS REFERENCE

This application is a National Stage entry (§ 371) application ofInternational Application No. PCT/US2020/018308, filed on Feb. 14, 2020,which claims the benefit of priority to U.S. Provisional Application No.62/794,225, filed Jan. 18, 2019, which is incorporated in its entirety.

INCORPORATION BY REFERENCE

All publications and patent documents mentioned herein are incorporatedby reference in their entirety.

FIELD

The present disclosure is related to devices and methods for improvingoptical analysis of a thin layer of a sample sandwiched betweencontaining between two plates.

BACKGROUND

Generating an area of light with uniform intensity is essential in a lotof applications, especially in imaging. Imaging requires auniform-light-intensity light illumination over the entire area of thesample under the field of view of an imager.

Accordingly, an object of this invention is to provide a device that canconvert a point light source into a uniform area light source.

BRIEF SUMMARY

The following brief summary is not intended to include all features andaspects of the present invention.

In one aspect, the present invention provides a planar area light sourcecomprising an end-emitting optical fiber including a first end and asecond end, a light extraction plate including a light scatteringstructure, and a light diffuser film disposed above the light scatteringstructure. The first end of the end-emitting optical fiber faces a lightsource to receive light. The second end of the end-emitting opticalfiber is embedded in the light extraction plate, such that the secondend emits light into the light extraction plate. The light scatteringstructure extracts light emitted into the light extraction plate, whichextracted light passes through the light diffuser film, therebyproviding a uniform light distribution over a surface area of the lightextraction plate.

In another aspect of the present invention, the planar area light sourcecomprises a side-emitting optical fiber including a first end and alight emitting sidewall, a light extraction plate including a lightscattering structure, and a light diffuser film disposed above the lightscattering structure. The first end of the side-emitting optical fiberfaces a light source to receive light. The side-emitting optical fiberextends laterally across an entire width of a first end of the lightextraction plate, such that a portion of the light emitting sidewall ispositioned within the light extraction plate and is configured to emitlight into the light extraction plate. The light scattering structureextracts light emitted into the light extraction plate, which extractlight passes through the light diffuser film, thereby providing auniform light distribution over a surface area of the light extractionplate.

In another aspect of the present invention, the planar area light sourcecomprises a side-emitting optical fiber including a first end, a secondend, and a light emitting sidewall, a light extraction plate including asurface having a light scattering structure, and a light diffuser filmdisposed above the light scattering structure. The first end and thesecond end of the side-emitting optical fiber face a light source toreceive light. The side-emitting optical fiber extends laterally acrossan entire width of a first end of the light extraction plate, such thata first portion of the light emitting sidewall is positioned within thelight extraction plate and is configured to emit light into the lightextraction plate. The side-emitting optical fibers extends laterallyacross an entire width of a second end of the light extraction plate,such that a second portion of the light emitting sidewall is positionedwithin the light extraction plate and is configured to emit light intothe light extraction plate. The light scattering structure extractslight emitted into the light extraction plate, which extracted lightpasses through the light diffuser film, thereby providing a uniformlight distribution over a surface area of the light extraction plate.

In another aspect of the present invention, the planar area light sourcecomprises a side-emitting optical fiber comprising a first end, a secondend, and a light emitting sidewall including a coated portion of whichis coated with a reflective material that prevents light from beingemitted from the coated portion of the side-emitting optical fiber, alight extraction plate including a surface having a light scatteringstructure, and a light diffuser film disposed above the light scatteringstructure. The first end and the second end of the side-emitting opticalfiber faces a light source to receive light. The side-emitting opticalfiber extends laterally across an entire width of a first end of thelight extraction plate, such that a first portion of the light emittingsidewall is positioned within the light extraction plate and isconfigured to emit light into the light extraction plate. Theside-emitting optical fibers extends laterally across an entire width ofa second end of the light extraction plate, such that a second portionof the light emitting sidewall is positioned within the light extractionplate and is configured to emit light into the light extraction plate.The reflective material is not coated over the first portion and thesecond portion of the light emitting sidewall. The light scatteringstructure extracts light emitted into the light extraction plate, whichextracted light passes through the light diffuser film, therebyproviding a uniform light distribution over a surface area of the lightextraction plate.

In another aspect of the present invention, the planar area light sourcecomprises a QMAX card, an end-emitting optical fiber or a side-emittingoptical fiber, a light extraction plate including a light scatteringstructure, a light diffuser film disposed above the light scatteringstructure, and an imager including an image sensor and a lens. An end ofthe either of the end-mitting or side-emitting optical fiber is orientedtowards the light source of the imager and the QMAX card is positionedin parallel with the light extraction plate of the device, such thatlight emitted from the light source of the imager is utilized touniformly illuminate a surface area of the QMAX card.

BRIEF DESCRIPTION OF THE DRAWINGS

A skilled artisan will understand that the drawings, described below,are for illustration purposes only. In some Figures, the drawings are inscale. For clarity purposes, some elements are enlarged when illustratedin the Figures. It should be noted that the Figures do not intend toshow the elements in strict proportion. The dimensions of the elementsshould be delineated from the descriptions herein provided andincorporated by reference. The drawings are not intended to limit thescope of the present invention in any way.

FIG. 1A shows a front view of the planar area light source according toone embodiment of the present invention.

FIG. 1B shows a top view of the planar area light source of FIG. 1A.

FIG. 2A shows a front view of the planar area light source according toanother embodiment of the present invention.

FIG. 2B shows a top view of the planar area light source of FIG. 2A.

FIG. 3A shows a front view of the planar area light source according toyet another embodiment of the present invention.

FIG. 3B shows a top view of the planar area light source of FIG. 3A.

FIG. 4 shows a front view of an alternative embodiment of the planararea light source according to one embodiment of the present invention.

FIG. 5 shows a schematic view of an imaging system including a planararea light source according to one embodiment of the present inventionbeing used to uniformly illuminate a QMAX device.

DETAILED DESCRIPTION

The following detailed description illustrates certain embodiments ofthe invention by way of example and not by way of limitation. If any,the section headings and any subtitles used herein are fororganizational purposes only and are not to be construed as limiting thesubject matter described in any way. The contents under a sectionheading and/or subtitle are not limited to the section heading and/orsubtitle, but apply to the entire description of the present invention.

The citation of any publication is for its disclosure prior to thefiling date and should not be construed as an admission that the presentclaims are not entitled to antedate such publication by virtue of priorinvention. Further, the dates of publication provided can be differentfrom the actual publication dates which can need to be independentlyconfirmed.

Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present teachings, some exemplarymethods and materials are now described.

The term “end-emitting optical fiber” refers to a long thin strand ofmaterial, i.e., plastic or silica, consisting of a transparent innercore and an external coating called a cladding. The transparent innercore allows light to travel unimpeded down the length of the fiber whilethe cladding acts like a one-way mirror, containing any light that triesto escape the fiber by bouncing it back into the core in a processcalled total internal reflection. This combination of core and claddingallows light to travel along the fiber for great distances, emerging atthe other end nearly as bright as the original source of illumination.

The term “side-emitting optical fiber” refers to a long thin strand ofmaterial, i.e., plastic or silica, consisting of a transparent innercore and an external coating called a cladding. “Side-emitting opticalfibers’ are different from “end-emitting optical fibers” because theircladding is intentionally less effective, i.e., the interface betweenthe cladding and the core layer is rougher, such that light graduallyescapes along the whole length of the fiber creating a fairly even glowthrough the fiber. Side-emitting fibers are more visible in ambientlight than end emitting fibers.

The term “light extraction plate” or “light guide plate” refers to atransparent panel or substrate that is flexible or rigid, comprisingpolycarbonate or acrylic, which includes structures on its front surfacethat direct light out of its front.

The term “light scattering structure” refers to the structures disposedon the “light extraction plate” or “light guide plate”. These “lightscattering structures” can be etched, imprinted, and/or printed in theform of line arrays, dot arrays, and/or microlens arrays. Moreover,these “light scattering structures” can be particulates added into thesubstrate and scattered therethroughout.

The term “light diffuser film” refers to a film or sheet of material,comprising plastic or silica, that is designed to break up andhomogenize light in order to distribute the light evenly.

The term “light emitting face” refers to the portion or area of the“end-emitting optical fiber” and “side-emitting optical fiber” thatemits lights.

The term “light coupling face” refers to portion or area of the“end-emitting optical fiber” and “side-emitting optical fiber” thatreceives light.

The terms “CROF Card (or card)”, “COF Card”, “QMAX-Card”, “Q-Card”,“CROF device”, “COF device”, “QMAX-device”, “CROF plates”, “COF plates”,and “QMAX-plates” are interchangeable, except that in some embodiments,the COF card does not comprise spacers; and the terms refer to a devicethat comprises a first plate and a second plate that are movablerelative to each other into different configurations (including an openconfiguration and a closed configuration), and that comprises spacers(except some embodiments of the COF card) that regulate the spacingbetween the plates. The term “X-plate” can refer to one of the twoplates in a CROF card, wherein the spacers are fixed to this plate. Moredescriptions of the COF Card, CROF Card, and X-plate are given in theprovisional application Ser. No. 62/456,065, filed on Feb. 7, 2017,which is incorporated herein in its entirety for all purposes.

The term “open configuration” of the two plates in a QMAX process meansa configuration in which the two plates are either partially orcompletely separated apart and the spacing between the plates is notregulated by the spacers

The term “closed configuration” of the two plates in a QMAX processmeans a configuration in which the plates are facing each other, thespacers and a relevant volume of the sample are between the plates, therelevant spacing between the plates, and thus the thickness of therelevant volume of the sample, is regulated by the plates and thespacers, wherein the relevant volume is at least a portion of an entirevolume of the sample.

The term “a sample thickness is regulated by the plate and the spacers”in a QMAX process means that for a give condition of the plates, thesample, the spacer, and the plate compressing method, the thickness ofat least a port of the sample at the closed configuration of the platescan be predetermined from the properties of the spacers and the plate.

The term “inner surface” or “sample surface” of a plate in a QMAX cardcan refer to the surface of the plate that touches the sample, while theother surface (that does not touch the sample) of the plate is termed“outer surface”.

The term “height” or “thickness” of an object in a QMAX process canrefer to, unless specifically stated, the dimension of the object thatis in the direction normal to a surface of the plate. For example,spacer height is the dimension of the spacer in the direction normal toa surface of the plate, and the spacer height and the spacer thicknessmeans the same thing.

The term “area” of an object in a QMAX process can refer to, unlessspecifically stated, the area of the object that is parallel to asurface of the plate. For example, spacer area is the area of the spacerthat is parallel to a surface of the plate.

The term of QMAX card can refer the device that perform a QMAX (e.g.CROF) process on a sample, and have or not have a hinge that connect thetwo plates.

The term “QMAX card with a hinge and “QMAX card” are interchangeable.

The term “angle self-maintain”, “angle self-maintaining”, or “rotationangle self-maintaining” can refer to the property of the hinge, whichsubstantially maintains an angle between the two plates, after anexternal force that moves the plates from an initial angle into theangle is removed from the plates.

The term “a spacer has a predetermined height” and “spacers have apredetermined inter-spacer distance” means, respectively, that the valueof the spacer height and the inter spacer distance is known prior to aQMAX process. It is not predetermined, if the value of the spacer heightand the inter-spacer distance is not known prior to a QMAX process. Forexample, in the case that beads are sprayed on a plate as spacers, wherebeads are landed at random locations of the plate, the inter-spacerdistance is not predetermined. Another example of not predeterminedinter spacer distance is that the spacers moves during a QMAX processes.

The term “a spacer is fixed on its respective plate” in a QMAX processmeans that the spacer is attached to a location of a plate and theattachment to that location is maintained during a QMAX (i.e. thelocation of the spacer on respective plate does not change) process. Anexample of “a spacer is fixed with its respective plate” is that aspacer is monolithically made of one piece of material of the plate, andthe location of the spacer relative to the plate surface does not changeduring the QMAX process. An example of “a spacer is not fixed with itsrespective plate” is that a spacer is glued to a plate by an adhesive,but during a use of the plate, during the QMAX process, the adhesivecannot hold the spacer at its original location on the plate surface andthe spacer moves away from its original location on the plate surface.

As will be apparent to those of skill in the art upon reading thisdisclosure, each of the individual embodiments described and illustratedherein has discrete components and features which can be readilyseparated from or combined with the features of any of the other severalembodiments without departing from the scope or spirit of the presentteachings. Any recited method can be carried out in the order of eventsrecited or in any other order which is logically possible. One skilledartisan will appreciate that the present invention is not limited in itsapplication to the details of construction, the arrangements ofcomponents, category selections, weightings, pre-determined signallimits, or the steps set forth in the description or drawings herein.The invention is capable of other embodiments and of being practiced orbeing carried out in many different ways.

Working Principles and Certain Exemplary Examples

Referring now to FIGS. 1A and 1B, there are shown front and top views ofthe planar area light source, respectively, according to one embodimentof the present invention. In one embodiment, the planar area lightsource 100 comprises an end-emitting optical fiber 1, a light source 2,a light extraction plate 3, and a light diffuser film 4. Theend-emitting optical fiber 1 is configured to couple light emitted fromthe light source 2, to the light extraction plate 3. In one embodiment,the end-emitting optical fiber 1 is composed of a polymer. In analternative embodiment, the end-emitting optical fiber 1 comprises aninorganic dielectric material, or silica glass. In one embodiment, theend-emitting optical fiber 1 includes a diameter that is coextensivewith the diameter and/or height of the light extraction plate 3.

The end-emitting optical fiber 1 comprises a first end including a lightcoupling face and a second opposing end including a light emitting face.The first end of the end-emitting optical fiber 1 extends outwardly fromthe light extraction plate 3 and faces the light source 2 and the secondend is embedded in an end of the light extraction plate 3. The lightemitted from the light source 2 enters the end-emitting optical fiber 1at the light coupling face. The light travels through the end-emittingoptical fiber 1 and then emits into the extraction plate 3 via the lightemitting face. The light beams B11 emitted from the light emitting faceof the end-emitting optical fiber 1 travel from one end of lightextraction plate 3 to the other end of the light extraction plate 3.While the light beams B11 travel through the light extraction plate 3,parts of the light beams B11 are extracted from the light extractionplate 3 via a light scattering structure 6 disposed on the surface ofthe light extraction plate 3. These extracted light beams form lightbeams B12. The light beams B12 then go through the light diffuser film4, which is disposed above the surface of the light extraction plate 3that extracts the light. The light diffuser film 4 makes the lightintensity of the extracted light beams B12 more uniformly distributedover the surface area of the light extraction plate 3. In oneembodiment, the light diffuser film 4 is disposed on the surface of thelight extraction plate 3. In another embodiment, the light diffuser film4 is adhered to the surface of the light extraction plate 3. In oneembodiment, the light diffuser film 4 is composed of grounded glass. Inalternative embodiments, the light diffuser film 4 comprisesmat-finished film, and/or semi-opaque white film.

Referring now to FIGS. 2A and 2B, there are shown front and top views ofthe planar area light source, respectively, according to anotherembodiment of the present invention. In one embodiment, the planar arealight source 200 comprises a side-emitting optical fiber 5, a lightsource 2, a light extraction plate 3, and a light diffuser film 4. Theside-emitting optical fiber 5 is configured to couple light emitted fromthe light source 2, to the light extraction plate 3. In one embodiment,the side-emitting optical fiber 5 is composed of a polymer. Inalternative embodiments, the side-emitting optical fiber 5 can comprisesan inorganic dielectric material, or silica glass. In one embodiment,the side-emitting optical fiber 5 includes a diameter that iscoextensive with the diameter and/or height of the light extractionplate 3.

The side-emitting optical fiber 5 includes a first end including a lightcoupling face, a second end, and a light emitting sidewall. Theside-emitting optical fiber 5 penetrates through a first side of thelight extraction plate 3 near an end of the light extraction plate 3 andexits an opposing second side of the light extraction plate 3, as shownby FIG. 2B, such that the side-emitting optical fiber 5 extendslaterally across the entire width of the first end of the lightextraction plate 3. In this way, the first end and the second end of theside-emitting optical fiber 5 are disposed outside of the lightextraction plate 3, and a portion 8 of the light emitting sidewall ofthe side-emitting optical fiber 5 is disposed within the lightextraction plate 3.

The light coupling face of the side-emitting optical fiber 5 facestowards the light source 2. The light emitted from the light source 2enters in into the side-emitting optical fiber 5 via the light couplingface and emits out into the extraction plate 3 from the portion 8 of thelight emitting sidewall of the side-emitting optical fiber 5. The lightbeams B21 emitted by the light emitting sidewall of the side-emittingoptical fiber 5 travel from one end of the light extraction plate 3 tothe other end of the light extraction plate 3. When light beams B21travel through the light extraction plate 3, parts of the light beamsB21 are extracted from the light extraction plate 3 by a lightscattering structure 6 disposed on the surface of light extraction plate3. These extracted light beams form light beams B22. The light beams B22then go through the light diffuser film 4, which is disposed above thesurface of the light extraction plate 3 that extracts the light. Thelight diffuser film 4 makes the light intensity of the extracted lightbeams B22 more uniformly distributed over the surface area of the lightextraction plate 3. In one embodiment, the light diffuser film 4 isdisposed on the surface of the light extraction plate 3. In anotherembodiment, the light diffuser film 4 is adhered to the surface of thelight extraction plate 3. In one embodiment, the light diffuser film 4is composed of grounded glass. In alternative embodiments, the lightdiffuser film 4 can comprise mat-finished film, and/or semi-opaque whitefilm.

Referring now to FIGS. 3A and 3B, there are shown front and top views ofthe planar area light source, respectively, according to yet anotherembodiment of the present invention. In one embodiment, the planar arealight source 300 comprises a side-emitting optical fiber 5, a lightsource 2, a light extraction plate 3 and a light diffuser film 4. Theside-emitting optical fiber 5 is configured to couple light emitted fromthe light source 2, to the light extraction plate 3. In one embodiment,the side-emitting optical fiber 5 is composed of a polymer. Inalternative embodiments, the side-emitting optical fiber 5 comprises aninorganic dielectric material, or silica glass. In one embodiment, theside-emitting optical fiber 5 includes a diameter that is coextensivewith the diameter and/or height of the light extraction plate 3.

The side-emitting optical fiber 5 includes a first end including a firstlight coupling face, a second end including a second light couplingface, and a light emitting sidewall. The side-emitting optical fiber 5penetrates twice through the light extraction plate 3. The side-emittingoptical fiber 5 first penetrates through a first side of the lightextraction plate 3 near a first end of the light extraction plate 3 andexits an opposing second side of the light extraction plate 3. Theside-emitting optical fiber penetrates a second time through an opposingsecond side of the light extraction plate 3 near an opposing second endof the light extraction plate 3 and exits the first side of the lightextraction plate 3, such that the first end and the second end of theside-emitting optical fiber 5 are disposed outside of the lightextraction plate 3. In this way, the side-emitting optical fiber 5 formsa first portion 10 of the light emitting sidewall that extends laterallyacross the entire width of a first end of the light extraction plate 3and a second portion 12 of the light emitting sidewall that extendslaterally across the entire width of the opposing second end of thelight extraction plate 3.

The first light coupling face of the first end and the second lightcoupling face of the second end of the side-emitting optical fiber 5face the light source 2 so as to receive light. The light emitted fromlight source 2 enters the side-emitting optical fiber 5 at both thefirst and the second light coupling faces. The light travels through theside-emitting optical fiber 5 and emits out into the extraction plate 3from the first and second portions 10, 12 of the light emitting sidewallof the side-emitting optical fiber 5 that are disposed within the lightextraction plate 3. The light beams B31 emitting from the first portion10 of the light emitting sidewall travel from the first end of lightextraction plate 3 to the second end of the light extraction plate 3.The light beams B32 emitted from the second portion 12 of the lightemitting sidewall travel from the second end of the light extractionplate 3 to the first end of the light extraction plate 3. When the lightbeams B31, B32 travel through light extraction plate 3, parts of themare extracted from the light extraction plate 3 by the light scatteringstructure 6 disposed at the surface of light extraction plate 3. Theseextracted light beams form light beams B33. The light beams B33 then gothrough the light diffuser film 4, which is disposed above the surfaceof the light extraction plate 3 that extracts the light. The lightdiffuser film 4 makes the light intensity of the extracted light beamsB33 more uniformly distributed over the surface area of the lightextraction plate 3. In one embodiment, the light diffuser film 4 isdisposed on the surface of the light extraction plate 3. In anotherembodiment, the light diffuser film 4 is adhered to the surface of thelight extraction plate 3. In one embodiment, the light diffuser film 4is composed of grounded glass. In alternative embodiments, the lightdiffuser film 4 comprises a mat-finished film, and/or a semi-opaquewhite film.

Referring now to FIG. 4 , there is shown an alternative embodiment ofthe planar area light source of FIGS. 3A and 3B. In one embodiment, theplanar area light source 400 includes a side-emitting optical fiber 5that is coated with a reflective material 7, except on the first andsecond portions 10, 12 of the light emitting sidewall of theside-emitting optical fiber 5 that are disposed within the lightextraction plate 3. The reflective material 7 prevents light travelingthrough the side-emitting optical fiber 5 from leaking and/or beingemitted from the portions of the light emitting optical fiber 5 that arenot in the light extraction plate. In this way, light energy loss isminimized, and the light being emitted from the uncoated first andsecond portions 10, 12 of the light emitting sidewall of theside-emitting optical fiber 5 is intensified.

Referring now to FIG. 5 , there is shown a schematic view of an imagingsystem including a planar area light source according to one embodimentof the present invention being used to illuminate a QMAX device, i.e.,QMAX card. In one embodiment of the present invention, the imagingsystem 600 comprises an imager 14, a QMAX card 16, and a planar arealight source 500. In one embodiment, a light coupling end of the opticalfiber 5 of the planar area light source 500 is oriented towards a lightsource so as to receive light. The QMAX card 16 is positioned inparallel with the light extraction plate 3 of the planar area lightsource 500. In this way, light emitted from the light source can beutilized to uniformly illuminate the surface area of the QMAX card 16.

Exemplary Embodiments of the Present Invention

-   -   1. A device, comprising:        -   (i) an end-emitting optical fiber including a first end and            a second end;        -   (ii) a light extraction plate including a light scattering            structure; and        -   (iii) a light diffuser film disposed above the light            scattering structure,            -   wherein the first end of the end-emitting optical fiber                faces a light source so as to receive light,            -   wherein the second end of the end-emitting optical fiber                is embedded in the light extraction plate, such that the                second end emits light into the light extraction plate,            -   wherein the light scattering structure extracts light                emitted into the light extraction plate, and            -   wherein the extracted light passes through the light                diffuser film, thereby providing a uniform light                distribution over a surface area of the light extraction                plate.    -   2. A device, comprising:        -   (i) a side-emitting optical fiber including a first end and            a light emitting sidewall;        -   (ii) a light extraction plate including a light scattering            structure; and        -   (iii) a light diffuser film disposed above the light            scattering structure,            -   wherein the first end of the side-emitting optical fiber                faces a light source so as to receive light,            -   wherein the side-emitting optical fiber extends                laterally across an entire width of an end of the light                extraction plate, such that a portion of the light                emitting sidewall is positioned within the light                extraction plate and is configured to emit light into                the light extraction plate,            -   wherein the light scattering structure extracts light                emitted into the light extraction plate, and            -   wherein the extracted light passes through the light                diffuser film, thereby providing a uniform light                distribution over a surface area of the light extraction                plate.    -   3. A device, comprising:        -   (i) a side-emitting optical fiber including a first end, a            second end, and a light emitting sidewall;        -   (ii) a light extraction plate including a surface having a            light scattering structure; and        -   (iii) a light diffuser film disposed above the light            scattering structure,            -   wherein the first end and the second end of the                side-emitting optical fiber face a light source so as to                receive light,            -   wherein the side-emitting optical fiber extends                laterally across an entire width of a first end of the                light extraction plate, such that a first portion of the                light emitting sidewall is positioned within the light                extraction plate and is configured to emit light into                the light extraction plate,            -   wherein the side-emitting optical fibers extends                laterally across an entire width of a second end of the                light extraction plate, such that a second portion of                the light emitting sidewall is positioned within the                light extraction plate and is configured to emit light                into the light extraction plate,            -   wherein the light scattering structure extracts light                emitted into the light extraction plate, and            -   wherein the extracted light passes through the light                diffuser film, thereby providing a uniform light                distribution over a surface area of the light extraction                plate.    -   4. A device, comprising:        -   (i) a side-emitting optical fiber comprising a first end, a            second end, and a light emitting sidewall including a coated            portion of which is coated with a reflective material that            prevents light from being emitted from the coated portion of            the side-emitting optical fiber;        -   (ii) a light extraction plate including a surface having a            light scattering structure; and        -   (iii) a light diffuser film disposed above the light            scattering structure,            -   wherein the first end and the second end of the                side-emitting optical fiber faces a light source so as                to receive light,            -   wherein the side-emitting optical fiber extends                laterally across an entire width of a first end of the                light extraction plate, such that a first portion of the                light emitting sidewall is positioned within the light                extraction plate and is configured to emit light into                the light extraction plate,            -   wherein the side-emitting optical fibers extends                laterally across an entire width of a second end of the                light extraction plate, such that a second portion of                the light emitting sidewall is positioned within the                light extraction plate and is configured to emit light                into the light extraction plate,            -   wherein the reflective material is not coated over the                first portion and the second portion of the light                emitting sidewall,            -   wherein the light scattering structure extracts light                emitted into the light extraction plate, and            -   wherein the extracted light passes through the light                diffuser film, thereby providing a uniform light                distribution over a surface area of the light extraction                plate.    -   5. A system, comprising:        -   (i) a QMAX card;        -   (ii) the device as in any prior claim; and        -   (iii) an imager including an image sensor and a lens,            -   wherein an end of the optical fiber of the device is                oriented towards a light source of the imager and the                QMAX card is positioned in parallel with the light                extraction plate of the device, such that light emitted                from the light source of the imager is utilized to                uniformly illuminate a surface area of the QMAX card.    -   6. The device or system as in any prior claim, further        comprising a light source.    -   7. The device or system as in any prior claim, wherein the        end-emitting optical fiber comprises a material selected from        the group consisting a polymer, an inorganic dielectric        material, and silica glass.    -   8. The device or system as in any prior claim, wherein the        side-emitting optical fiber comprises a material selected from        the group consisting a polymer, an inorganic dielectric        material, and silica glass.    -   9. The device or system as in any prior claim, wherein the        end-emitting optical fiber comprises a transmission of 0.5-5% at        the interface between a core and a cladding layer of the        end-emitting optical fiber.    -   10. The device or system as in any prior claim, wherein the        side-emitting optical fiber comprises a transmission of 0.5-5%        at the interface between a core and a cladding layer of the        optical fiber.    -   11. The device or system as in any prior claim, wherein the        diameter of the end-emitting optical fiber is coextensive with        the smallest dimension of the light extraction plate.    -   12. The device or system as in any prior claim, wherein the        diameter of the side-emitting optical fiber is coextensive with        the smallest dimension of the light extraction plate.    -   13. The device or system as in any prior claim, wherein the        length of the end-emitting optical fiber is 10 mm, 50 mm, 100        mm, 200 mm, 500 mm, or any value therebetween.    -   14. The device or system as in any prior claim, wherein the        length of the side-emitting optical fiber is 10 mm, 50 mm, 100        mm, 200 mm, 500 mm, or any value therebetween.    -   15. The device or system as in any prior claim, wherein the        diameter of the end-emitting optical fiber is 1.5 mm.    -   16. The device or system as in any prior claim, wherein the        diameter of the side-emitting optical fiber is 1.5 mm    -   17. The device or system as in any prior claim, wherein the        diameter of the end-emitting optical fiber is 1 um, 10 um, 100        um, 1 mm, 10 mm, or any value therebetween.    -   18. The device or system as in any prior claim, wherein the        diameter of the side-emitting optical fiber is 1 um, 10 um, 100        um, 1 mm, 10 mm, or any value therebetween.    -   19. The device or system as in any prior claim, wherein the        light extraction plate includes a thickness of 500 um, 1 mm, 2        mm, 4 mm, 5 mm, 10 mm, or any value therebetween.    -   20. The device or system as in any prior claim, wherein the        light extraction plate includes a thickness of 2 mm.    -   21. The device or system as in any prior claim, wherein the        light extraction plate includes a surface dimension of 12 mm×36        mm.    -   22. The device or system as in any prior claim, wherein the        light extraction plate includes a surface area of 1        cm{circumflex over ( )}2, 10 cm{circumflex over ( )}2, 100        cm{circumflex over ( )}2, 1000 cm{circumflex over ( )}2, or any        value therebetween.    -   23. The device or system as in any prior claim, wherein the        light extraction plate comprises a transparent panel.    -   24. The device or system as in any prior claim, wherein the        light extraction plate includes a material selected from the        group consisting of acrylic, glass, and plastic polymer.    -   25. The device or system as in any prior claim, wherein the        distance between the first portion of the light emitting        sidewall and the second portion of the light emitting sidewall        is larger than the lateral dimension of a field of view of an        imager.    -   26. The device or system as in any prior claim, wherein the        distance between the first portion of the light emitting        sidewall and the second portion of the light emitting sidewall        is 30 mm.    -   27. The device or system as in any prior claim, wherein the        distance between the first portion of the light emitting        sidewall and the second portion of the light emitting sidewall        is 5 mm, 10 mm, 20 mm, 100 mm, or any value therebetween.    -   28. The device or system as in any prior claim, wherein the        light extraction plate is configured to extract the light        travelling therein from at least one of its surfaces.    -   29. The device or system as in any prior claim, the light        diffuser film is selected from the group consisting of opaque        white plastic, ground glass, and textured plastic film.    -   30. The device or system as in any prior claim, the distance        between the light diffuser film and the light extraction plate        is close contact.    -   31. The device or system as in any prior claim, wherein the        light diffuser film is adhered to the surface of the light        extraction plate.    -   32. The device or system as in any prior claim, wherein the        distance between the diffuser film and the light extraction        plate is 100 um, 1 mm, 2 mm, 5 mm, 10 mm, or any value        therebetween.    -   33. The device or system as in any prior claim, wherein the        light scattering structure is a structure selected from the        group consisting of line arrays, dot arrays, and microlens        arrays.    -   34. The device or system as in any prior claim, wherein the        light scattering structure is etched, imprinted, printed, or any        combination thereof.    -   35. The device or system as in any prior claim, wherein the        light scattering structure comprise particulates scattered        throughout the light scattering plate.    -   36. The device or system as in any prior claim claim 35, wherein        the particulates comprise any structure having a different        reflective index than the light scattering plate.    -   37. The device or system as in any prior claim, wherein the        particulates are selected from the group consisting of air        bubbles, vacuum sealed areas, plastics, and polymers.    -   38. The device or system as in any prior claim, wherein the        light scattering structure is selected from the group consisting        of random textured surfaces, periodic gratings, painted white        dots, microparticles, and nanoparticles.    -   39. The device or system as in any prior claim, the light source        is selected from the group consisting of LED, laser, and        incandescent light bulb.    -   40. The system as in any prior claim, wherein the distance        between the QMAX card and the device is less than 5 mm.    -   41. The system as in any prior claim, wherein the QMAX card is        positioned between the imager and the light extraction plate.        QMAX System

A) QMAX Card

Details of the QMAX card are described in detail in a variety ofpublications including International Application No. PCT/US2016/046437,which is hereby incorporated by reference herein for all purposes.

I. Plates

In present invention, generally, the plates of CROF are made of anymaterial that (i) is capable of being used to regulate, together withthe spacers, the thickness of a portion or entire volume of the sample,and (ii) has no significant adverse effects to a sample, an assay, or agoal that the plates intend to accomplish. However, in certainembodiments, particular materials (hence their properties) ae used forthe plate to achieve certain objectives.

In certain embodiments, the two plates have the same or differentparameters for each of the following parameters: plate material, platethickness, plate shape, plate area, plate flexibility, plate surfaceproperty, and plate optical transparency.

(i) Plate Materials.

The plates are made a single material, composite materials, multiplematerials, multilayer of materials, alloys, or a combination thereof.Each of the materials for the plate is an inorganic material, am organicmaterial, or a mix, wherein examples of the materials are given inparagraphs of Mat-1 and Mat-2.

Mat-1: The inorganic materials for the plates include, not limited to,glass, quartz, oxides, silicon-dioxide, silicon-nitride, hafnium oxide(HfO), aluminum oxide (AlO), semiconductors: (silicon, GaAs, GaN, etc.),metals (e.g. gold, silver, coper, aluminum, Ti, Ni, etc.), ceramics, orany combinations of thereof.

Mat-2: The organic materials for the spacers include, not limited to,polymers (e.g. plastics) or amorphous organic materials. The polymermaterials for the spacers include, not limited to, acrylate polymers,vinyl polymers, olefin polymers, cellulosic polymers, noncellulosicpolymers, polyester polymers, Nylon, cyclic olefin copolymer (COC),poly(methyl methacrylate) (PMMA), polycarbonate (PC), cyclic olefinpolymer (COP), liquid crystalline polymer (LCP), polyimide (PA),polyethylene (PE), polyimide (PI), polypropylene (PP), poly(phenyleneether) (PPE), polystyrene (PS), polyoxymethylene (POM), polyether etherketone (PEEK), polyether sulfone (PES), poly(ethylene phthalate) (PET),polytetrafluoroethylene (PTFE), polyvinyl chloride (PVC), polyvinylidenefluoride (PVDF), polybutylene terephthalate (PBT), fluorinated ethylenepropylene (FEP), perfluoroalkoxyalkane (PFA), polydimethylsiloxane(PDMS), rubbers, or any combinations of thereof.

In certain embodiments, the plates are each independently made of atleast one of glass, plastic, ceramic, and metal. In certain embodiments,each plate independently includes at least one of glass, plastic,ceramic, and metal.

In certain embodiments, one plate is different from the other plate inlateral area, thickness, shape, materials, or surface treatment. Incertain embodiments, one plate is the same as the other plate in lateralarea, thickness, shape, materials, or surface treatment.

The materials for the plates are rigid, flexible or any flexibilitybetween the two. The rigid (e.g. stiff) or flexibility is relative to agive pressing forces used in bringing the plates into the closedconfiguration.

In certain embodiments, a selection of rigid or flexible plate aredetermined from the requirements of controlling a uniformity of thesample thickness at the closed configuration.

In certain embodiments, at least one of the two plates are transparent(to a light). In certain embodiments at least a part or several parts ofone plate or both plates are transparent. In certain embodiments, theplates are non-transparent.

(ii) Plate Thickness.

In certain embodiments, the average thicknesses for at least one of theplates are 2 nm or less, 10 nm or less, 100 nm or less, 500 nm or less,1000 nm or less, 2 um (micron) or less, 5 um or less, 10 um or less, 20um or less, 50 um or less, 100 um or less, 150 um or less, 200 um orless, 300 um or less, 500 um or less, 800 um or less, 1 mm (millimeter)or less, 2 mm or less, 3 mm or less, or a range between any two of thevalues.

In certain embodiments, the average thicknesses for at least one of theplates are at most 3 mm (millimeter), at most 5 mm, at most 10 mm, atmost 20 mm, at most 50 mm, at most 100 mm, at most 500 mm, or a rangebetween any two of the values.

In certain embodiments, the thickness of a plate is not uniform acrossthe plate. Using a different plate thickness at different location canbe used to control the plate bending, folding, sample thicknessregulation, and others.

(iii) Plate Shape and Area.

Generally, the plates can have any shapes, as long as the shape allows acompress open flow of the sample and the regulation of the samplethickness. However, in certain embodiments, a particular shape can beadvantageous. The shape of the plate can be round, elliptical,rectangles, triangles, polygons, ring-shaped, or any superpositions ofthese shapes.

In certain embodiments, the two plates can have the same size or shape,or different. The area of the plates depend on the application. The areaof the plate is at most 1 mm2 (millimeter square), at most 10 mm2, atmost 100 mm2, at most 1 cm2 (centimeter square), at most 5 cm2, at most10 cm2, at most 100 cm2, at most 500 cm2, at most 1000 cm2, at most 5000cm2, at most 10,000 cm2, or over 10,000 cm2, or any arrange between anyof the two values. The shape of the plate can be rectangle, square,round, or others.

In certain embodiments, at least one of the plates is in the form of abelt (or strip) that has a width, thickness, and length. The width is atmost 0.1 cm (centimeter), at most 0.5 cm, at most 1 cm, at most 5 cm, atmost 10 cm, at most 50 cm, at most 100 cm, at most 500 cm, at most 1000cm, or a range between any two of the values. The length can be as longit needed. The belt can be rolled into a roll.

(iv) Plate Surface Flatness.

In many embodiments, an inner surface of the plates are flat orsignificantly flat, planar. In certain embodiments, the two innersurfaces are, at the closed configuration, parallel with each other.Flat inner surfaces facilitates a quantification and/or controlling ofthe sample thickness by simply using the predetermined spacer height atthe closed configuration. For non-flat inner surfaces of the plate, oneneed to know not only the spacer height, but also the exact the topologyof the inner surface to quantify and/or control the sample thickness atthe closed configuration. To know the surface topology needs additionalmeasurements and/or corrections, which can be complex, time consuming,and costly.

A flatness of the plate surface is relative to the final samplethickness (the final thickness is the thickness at the closedconfiguration), and is often characterized by the term of “relativesurface flatness” is the ratio of the plate surface flatness variationto the final sample thickness.

In certain embodiments, the relative surface is less than 0.01%, 0.1%,less than 0.5%, less than 1%, less than 2%, less than 5%, less than 10%,less than 20%, less than 30%, less than 50%, less than 70%, less than80%, less than 100%, or a range between any two of these values.

(v) Plate Surface Parallelness.

In certain embodiments, the two surfaces of the plate is significantlyparallel with each other. In certain embodiments, the two surfaces ofthe plate is not parallel with each other.

(vi) Plate Flexibility.

In certain embodiments, a plate is flexible under the compressing of aCROF process. In certain embodiments, both plates are flexible under thecompressing of a CROF process. In certain embodiments, a plate is rigidand another plate is flexible under the compressing of a CROF process.In certain embodiments, both plates are rigid. In certain embodiments,both plate are flexible but have different flexibility.

(vii) Plate Optical Transparency.

In certain embodiments, a plate is optical transparent. In certainembodiments, both plates are optical transparent. In certainembodiments, a plate is optical transparent and another plate is opaque.In certain embodiments, both plates are opaque. In certain embodiments,both plate are optical transparent but have different opticaltransparency. The optical transparency of a plate can refer to a part orthe entire area of the plate.

(viii) Surface Wetting Properties.

In certain embodiments, a plate has an inner surface that wets (e.g.contact angle is less 90 degree) the sample, the transfer liquid, orboth. In certain embodiments, both plates have an inner surface thatwets the sample, the transfer liquid, or both; either with the same ordifferent wettability. In certain embodiments, a plate has an innersurface that wets the sample, the transfer liquid, or both; and anotherplate has an inner surface that does not wet (e.g. the contact angleequal to or larger than 90 degree). The wetting of a plate inner surfacecan refer to a part or the entire area of the plate.

In certain embodiments, the inner surface of the plate has other nano ormicrostructures to control a lateral flow of a sample during a CROF. Thenano or microstructures include, but not limited to, channels, pumps,and others. Nano and microstructures are also used to control thewetting properties of an inner surface.

II. Spacers

(i) Spacers' Function.

In present invention, the spacers are configured to have one or anycombinations of the following functions and properties: the spacers areconfigured to (1) control, together with the plates, the thickness ofthe sample or a relevant volume of the sample (Preferably, the thicknesscontrol is precise, or uniform or both, over a relevant area); (2) allowthe sample to have a compressed regulated open flow (CROF) on platesurface; (3) not take significant surface area (volume) in a givensample area (volume); (4) reduce or increase the effect of sedimentationof particles or analytes in the sample; (5) change and/or control thewetting propertied of the inner surface of the plates; (6) identify alocation of the plate, a scale of size, and/or the information relatedto a plate, or (7) do any combination of the above.

(ii) Spacer Architectures and Shapes.

To achieve desired sample thickness reduction and control, in certainembodiments, the spacers are fixed its respective plate. In general, thespacer can have any shape, as long as the spacers are capable ofregulating the sample thickness during a CROF process, but certainshapes are preferred to achieve certain functions, such as betteruniformity, less overshoot in pressing, etc.

The spacer(s) is a single spacer or a plurality of spacers. (e.g. anarray). Certain embodiments of a plurality of spacers is an array ofspacers (e.g. pillars), where the inter-spacer distance is periodic oraperiodic, or is periodic or aperiodic in certain areas of the plates,or has different distances in different areas of the plates.

There are two kinds of the spacers: open-spacers and enclosed-spacers.The open-spacer is the spacer that allows a sample to flow through thespacer (e.g. the sample flows around and pass the spacer. For example, apost as the spacer.), and the enclosed spacer is the spacer that stopthe sample flow (e.g. the sample cannot flow beyond the spacer. Forexample, a ring shape spacer and the sample is inside the ring.). Bothtypes of spacers use their height to regular the final sample thicknessat a closed configuration.

In certain embodiments, the spacers are open-spacers only. In certainembodiments, the spacers are enclosed-spacers only. In certainembodiments, the spacers are a combination of open-spacers andenclosed-spacers.

The term “pillar spacer” means that the spacer has a pillar shape andthe pillar shape can refer to an object that has height and a lateralshape that allow a sample to flow around it during a compressed openflow.

In certain embodiments, the lateral shapes of the pillar spacers are theshape selected from the groups of (i) round, elliptical, rectangles,triangles, polygons, ring-shaped, star-shaped, letter-shaped (e.g.L-shaped, C-shaped, the letters from A to Z), number shaped (e.g. theshapes like 0 1, 2, 3, 4, . . . to 9); (ii) the shapes in group (i) withat least one rounded corners; (iii) the shape from group (i) withzig-zag or rough edges; and (iv) any superposition of (i), (ii) and(iii). For multiple spacers, different spacers can have differentlateral shape and size and different distance from the neighboringspacers.

In certain embodiments, the spacers can be and/or can include posts,columns, beads, spheres, and/or other suitable geometries. The lateralshape and dimension (e.g., transverse to the respective plate surface)of the spacers can be anything, except, in certain embodiments, thefollowing restrictions: (i) the spacer geometry will not cause asignificant error in measuring the sample thickness and volume; or (ii)the spacer geometry would not prevent the out-flowing of the samplebetween the plates (e.g. it is not in enclosed form). But in certainembodiments, they require some spacers to be closed spacers to restrictthe sample flow.

In certain embodiments, the shapes of the spacers have rounded corners.For example, a rectangle shaped spacer has one, several or all cornersrounded (like a circle rather 90 degree angle). A round corner oftenmake a fabrication of the spacer easier, and in some cases less damageto a biological material.

The sidewall of the pillars can be straight, curved, sloped, ordifferent shaped in different section of the sidewall. In certainembodiments, the spacers are pillars of various lateral shapes,sidewalls, and pillar-height to pillar lateral area ratio. In apreferred embodiment, the spacers have shapes of pillars for allowingopen flow.

(iii) Spacers' Materials.

In the present invention, the spacers are generally made of any materialthat is capable of being used to regulate, together with the two plates,the thickness of a relevant volume of the sample. In certainembodiments, the materials for the spacers are different from that forthe plates. In certain embodiments, the materials for the spaces are atleast the same as a part of the materials for at least one plate.

The spacers are made a single material, composite materials, multiplematerials, multilayer of materials, alloys, or a combination thereof.Each of the materials for the spacers is an inorganic material, amorganic material, or a mix, wherein examples of the materials are givenin paragraphs of Mat-1 and Mat-2. In a preferred embodiment, the spacersare made in the same material as a plate used in CROF.

(iv) Spacers' Mechanical Strength and Flexibility.

In certain embodiments, the mechanical strength of the spacers arestrong enough, so that during the compression and at the closedconfiguration of the plates, the height of the spacers is the same orsignificantly same as that when the plates are in an open configuration.In certain embodiments, the differences of the spacers between the openconfiguration and the closed configuration can be characterized andpredetermined.

The material for the spacers is rigid, flexible or any flexibilitybetween the two. The rigid is relative to a give pressing forces used inbringing the plates into the closed configuration: if the space does notdeform greater than 1% in its height under the pressing force, thespacer material is regarded as rigid, otherwise a flexible. When aspacer is made of material flexible, the final sample thickness at aclosed configuration still can be predetermined from the pressing forceand the mechanical property of the spacer.

(v) Spacers Inside Sample.

To achieve desired sample thickness reduction and control, particularlyto achieve a good sample thickness uniformity, in certain embodiments,the spacers are placed inside the sample, or the relevant volume of thesample. In certain embodiments, there are one or more spacers inside thesample or the relevant volume of the sample, with a proper inter spacerdistance. In certain embodiments, at least one of the spacers is insidethe sample, at least two of the spacers inside the sample or therelevant volume of the sample, or at least of “n” spacers inside thesample or the relevant volume of the sample, where “n” can be determinedby a sample thickness uniformity or a required sample flow propertyduring a CROF.

(vi) Spacer Height.

In certain embodiments, all spacers have the same pre-determined height.In certain embodiments, spacers have different pre-determined height. Incertain embodiments, spacers can be divided into groups or regions,wherein each group or region has its own spacer height. And in certainembodiments, the predetermined height of the spacers is an averageheight of the spacers. In certain embodiments, the spacers haveapproximately the same height. In certain embodiments, a percentage ofnumber of the spacers have the same height.

The height of the spacers is selected by a desired regulated finalsample thickness and the residue sample thickness. The spacer height(the predetermined spacer height) and/or sample thickness is 3 nm orless, 10 nm or less, 50 nm or less, 100 nm or less, 200 nm or less, 500nm or less, 800 nm or less, 1000 nm or less, 1 um or less, 2 um or less,3 um or less, 5 um or less, 10 um or less, 20 um or less, 30 um or less,50 um or less, 100 um or less, 150 um or less, 200 um or less, 300 um orless, 500 um or less, 800 um or less, 1 mm or less, 2 mm or less, 4 mmor less, or a range between any two of the values.

The spacer height and/or sample thickness is between 1 nm to 100 nm inone preferred embodiment, 100 nm to 500 nm in another preferredembodiment, 500 nm to 1000 nm in a separate preferred embodiment, 1 um(e.g. 1000 nm) to 2 um in another preferred embodiment, 2 um to 3 um ina separate preferred embodiment, 3 um to 5 um in another preferredembodiment, 5 um to 10 um in a separate preferred embodiment, and 10 umto 50 um in another preferred embodiment, 50 um to 100 um in a separatepreferred embodiment.

In certain embodiments, the spacer height and/or sample thickness (i)equal to or slightly larger than the minimum dimension of an analyte, or(ii) equal to or slightly larger than the maximum dimension of ananalyte. The “slightly larger” means that it is about 1% to 5% largerand any number between the two values.

In certain embodiments, the spacer height and/or sample thickness islarger than the minimum dimension of an analyte (e.g. an analyte has ananisotropic shape), but less than the maximum dimension of the analyte.

For example, the red blood cell has a disk shape with a minim dimensionof 2 um (disk thickness) and a maximum dimension of 11 um (a diskdiameter). In an embodiment of the present invention, the spacers isselected to make the inner surface spacing of the plates in a relevantarea to be 2 um (equal to the minimum dimension) in one embodiment, 2.2um in another embodiment, or 3 (50% larger than the minimum dimension)in other embodiment, but less than the maximum dimension of the redblood cell. Such embodiment has certain advantages in blood cellcounting. In one embodiment, for red blood cell counting, by making theinner surface spacing at 2 or 3 um and any number between the twovalues, a undiluted whole blood sample is confined in the spacing, onaverage, each red blood cell (RBC) does not overlap with others,allowing an accurate counting of the red blood cells visually. (Too manyoverlaps between the RBC's can cause serious errors in counting).

In the present invention, in certain embodiments, it uses the plates andthe spacers to regulate not only a thickness of a sample, but also theorientation and/or surface density of the analytes/entity in the samplewhen the plates are at the closed configuration. When the plates are ata closed configuration, a thinner thickness of the sample gives a lessthe analytes/entity per surface area (e.g. less surface concentration).

(vii) Spacer Lateral Dimension.

For an open-spacer, the lateral dimensions can be characterized by itslateral dimension (sometime being called width) in the x and y-twoorthogonal directions. The lateral dimension of a spacer in eachdirection is the same or different. In certain embodiments, the lateraldimension for each direction (x or y) is . . . .

In certain embodiments, the ratio of the lateral dimensions of x to ydirection is 1, 1.5, 2, 5, 10, 100, 500, 1000, 10,000, or a rangebetween any two of the value. In certain embodiments, a different ratiois used to regulate the sample flow direction; the larger the ratio, theflow is along one direction (larger size direction).

In certain embodiments, the different lateral dimensions of the spacersin x and y direction are used as (a) using the spacers as scale-markersto indicate the orientation of the plates, (b) using the spacers tocreate more sample flow in a preferred direction, or both.

In a preferred embodiment, the period, width, and height.

In certain embodiments, all spacers have the same shape and dimensions.In certain embodiments, each of the spacers have different lateraldimensions.

For enclosed-spacers, in certain embodiments, the inner lateral shapeand size are selected based on the total volume of a sample to beenclosed by the enclosed spacer(s), wherein the volume size has beendescribed in the present disclosure; and in certain embodiments, theouter lateral shape and size are selected based on the needed strengthto support the pressure of the liquid against the spacer and thecompress pressure that presses the plates.

(viii) Aspect Ratio of Height to the Average Lateral Dimension of PillarSpacer.

In certain embodiments, the aspect ratio of the height to the averagelateral dimension of the pillar spacer is 100,000, 10,000, 1,000, 100,10, 1, 0.1, 0.01, 0.001, 0.0001, 0, 00001, or a range between any two ofthe values.

(ix) Spacer Height Precisions.

The spacer height should be controlled precisely. The relative precisionof the spacer (e.g. the ratio of the deviation to the desired spacerheight) is 0.001% or less, 0.01% or less, 0.1% or less; 0.5% or less, 1%or less, 2% or less, 5% or less, 8% or less, 10% or less, 15% or less,20% or less, 30% or less, 40% or less, 50% or less, 60% or less, 70% orless, 80% or less, 90% or less, 99.9% or less, or a range between any ofthe values.

(x) Inter-Spacer Distance.

The spacers can be a single spacer or a plurality of spacers on theplate or in a relevant area of the sample. In certain embodiments, thespacers on the plates are configured and/or arranged in an array form,and the array is a periodic, non-periodic array or periodic in somelocations of the plate while non-periodic in other locations.

In certain embodiments, the periodic array of the spacers has a latticeof square, rectangle, triangle, hexagon, polygon, or any combinations ofthereof, where a combination means that different locations of a platehas different spacer lattices.

In certain embodiments, the inter-spacer distance of a spacer array isperiodic (e.g. uniform inter-spacer distance) in at least one directionof the array. In certain embodiments, the inter-spacer distance isconfigured to improve the uniformity between the plate spacing at aclosed configuration.

The distance between neighboring spacers (e.g. the inter-spacerdistance) is 1 um or less, 5 um or less, 10 um or less, 20 um or less,30 um or less, 40 um or less, 50 um or less, 60 um or less, 70 um orless, 80 um or less, 90 um or less, 100 um or less, 200 um or less, 300um or less, 400 um or less, or a range between any two of the values.

In certain embodiments, the inter-spacer distance is at 400 or less, 500or less, 1 mm or less, 2 mm or less, 3 mm or less, 5 mm or less, 7 mm orless, 10 mm or less, or any range between the values. In certainembodiments, the inter-spacer distance is a 10 mm or less, 20 mm orless, 30 mm or less, 50 mm or less, 70 mm or less, 100 mm or less, orany range between the values.

The distance between neighboring spacers (e.g. the inter-spacerdistance) is selected so that for a given properties of the plates and asample, at the closed-configuration of the plates, the sample thicknessvariation between two neighboring spacers is, in certain embodiments, atmost 0.5%, 1%, 5%, 10%, 20%, 30%, 50%, 80%, or any range between thevalues; or in certain embodiments, at most 80%, 100%, 200%, 400%, or arange between any two of the values.

Clearly, for maintaining a given sample thickness variation between twoneighboring spacers, when a more flexible plate is used, a closerinter-spacer distance is needed.

Specify the accuracy of the inter spacer distance.

In a preferred embodiment, the spacer is a periodic square array,wherein the spacer is a pillar that has a height of 2 to 4 um, anaverage lateral dimension of from 5 to 20 um, and inter-spacer spacingof 1 um to 100 um.

In a preferred embodiment, the spacer is a periodic square array,wherein the spacer is a pillar that has a height of 2 to 4 um, anaverage lateral dimension of from to 20 um, and inter-spacer spacing of100 um to 250 um.

In a preferred embodiment, the spacer is a periodic square array,wherein the spacer is a pillar that has a height of 4 to 50 um, anaverage lateral dimension of from to 20 um, and inter-spacer spacing of1 um to 100 um.

In a preferred embodiment, the spacer is a periodic square array,wherein the spacer is a pillar that has a height of 4 to 50 um, anaverage lateral dimension of from to 20 um, and inter-spacer spacing of100 um to 250 um.

The period of spacer array is between 1 nm to 100 nm in one preferredembodiment, 100 nm to 500 nm in another preferred embodiment, 500 nm to1000 nm in a separate preferred embodiment, 1 um (e.g. 1000 nm) to 2 umin another preferred embodiment, 2 um to 3 um in a separate preferredembodiment, 3 um to 5 um in another preferred embodiment, 5 um to 10 umin a separate preferred embodiment, and 10 um to 50 um in anotherpreferred embodiment, 50 um to 100 um in a separate preferredembodiment, 100 um to 175 um in a separate preferred embodiment, and 175um to 300 um in a separate preferred embodiment.

(xi) Spacer Density.

The spacers are arranged on the respective plates at a surface densityof greater than one per um², greater than one per 10 um², greater thanone per 100 um², greater than one per 500 um², greater than one per 1000um², greater than one per 5000 um², greater than one per 0.01 mm²,greater than one per 0.1 mm², greater than one per 1 mm², greater thanone per 5 mm², greater than one per 10 mm², greater than one per 100mm², greater than one per 1000 mm², greater than one per 10000 mm², or arange between any two of the values.

(3) the spacers are configured to not take significant surface area(volume) in a given sample area (volume);

(xii) Ratio of Spacer Volume to Sample Volume.

In many embodiments, the ratio of the spacer volume (e.g. the volume ofthe spacer) to sample volume (e.g. the volume of the sample), and/or theratio of the volume of the spacers that are inside of the relevantvolume of the sample to the relevant volume of the sample are controlledfor achieving certain advantages. The advantages include, but notlimited to, the uniformity of the sample thickness control, theuniformity of analytes, the sample flow properties (e.g. flow speed,flow direction, etc.).

In certain embodiments, the ratio of the spacer volume r) to samplevolume, and/or the ratio of the volume of the spacers that are inside ofthe relevant volume of the sample to the relevant volume of the sampleis less than 100%, at most 99%, at most 70%, at most 50%, at most 30%,at most 10%, at most 5%, at most 3% at most 1%, at most 0.1%, at most0.01%, at most 0.001%, or a range between any of the values.

(xiii) Spacers Fixed to Plates.

The inter spacer distance and the orientation of the spacers, which playa key role in the present invention, are preferably maintained duringthe process of bringing the plates from an open configuration to theclosed configuration, and/or are preferably predetermined before theprocess from an open configuration to a closed configuration.

In certain embodiments of the present disclosure, spacers are fixed onone of the plates before bring the plates to the closed configuration.The term “a spacer is fixed with its respective plate” means that thespacer is attached to a plate and the attachment is maintained during ause of the plate. An example of “a spacer is fixed with its respectiveplate” is that a spacer is monolithically made of one piece of materialof the plate, and the position of the spacer relative to the platesurface does not change. An example of “a spacer is not fixed with itsrespective plate” is that a spacer is glued to a plate by an adhesive,but during a use of the plate, the adhesive cannot hold the spacer atits original location on the plate surface (e.g. the spacer moves awayfrom its original position on the plate surface).

In certain embodiments, at least one of the spacers are fixed to itsrespective plate. In certain embodiments, at two spacers are fixed toits respective plates. In certain embodiments, a majority of the spacersare fixed with their respective plates. In certain embodiments, all ofthe spacers are fixed with their respective plates.

In certain embodiments, a spacer is fixed to a plate monolithically.

In certain embodiments, the spacers are fixed to its respective plate byone or any combination of the following methods and/or configurations:attached to, bonded to, fused to, imprinted, and etched.

The term “imprinted” means that a spacer and a plate are fixedmonolithically by imprinting (e.g. embossing) a piece of a material toform the spacer on the plate surface. The material can be single layerof a material or multiple layers of the material.

The term “etched” means that a spacer and a plate are fixedmonolithically by etching a piece of a material to form the spacer onthe plate surface. The material can be single layer of a material ormultiple layers of the material.

The term “fused to” means that a spacer and a plate are fixedmonolithically by attaching a spacer and a plate together, the originalmaterials for the spacer and the plate fused into each other, and thereis clear material boundary between the two materials after the fusion.

The term “bonded to” means that a spacer and a plate are fixedmonolithically by binding a spacer and a plate by adhesion.

The term “attached to” means that a spacer and a plate are connectedtogether.

In certain embodiments, the spacers and the plate are made in the samematerials. In other embodiment, the spacers and the plate are made fromdifferent materials. In other embodiment, the spacer and the plate areformed in one piece. In other embodiment, the spacer has one end fixedto its respective plate, while the end is open for accommodatingdifferent configurations of the two plates.

In other embodiment, each of the spacers independently is at least oneof attached to, bonded to, fused to, imprinted in, and etched in therespective plate. The term “independently” means that one spacer isfixed with its respective plate by a same or a different method that isselected from the methods of attached to, bonded to, fused to, imprintedin, and etched in the respective plate.

In certain embodiments, at least a distance between two spacers ispredetermined (“predetermined inter-spacer distance” means that thedistance is known when a user uses the plates.).

In certain embodiments of all methods and devices described herein,there are additional spacers besides to the fixed spacers.

(xiv) Specific Sample Thickness.

In present invention, it was observed that a larger plate holding force(e.g. the force that holds the two plates together) can be achieved byusing a smaller plate spacing (for a given sample area), or a largersample area (for a given plate-spacing), or both.

In certain embodiments, at least one of the plates is transparent in aregion encompassing the relevant area, each plate has an inner surfaceconfigured to contact the sample in the closed configuration; the innersurfaces of the plates are substantially parallel with each other, inthe closed configuration; the inner surfaces of the plates aresubstantially planar, except the locations that have the spacers; or anycombination of thereof.

The spacers can be fabricated on a plate in a variety of ways, usinglithography, etching, embossing (nanoimprint), depositions, lift-off,fusing, or a combination of thereof. In certain embodiments, the spacersare directly embossed or imprinted on the plates. In certainembodiments, the spacers imprinted into a material (e.g. plastics) thatis deposited on the plates. In certain embodiments, the spacers are madeby directly embossing a surface of a CROF plate. The nanoimprinting canbe done by roll to roll technology using a roller imprinter, or roll toa planar nanoimprint. Such process has a great economic advantage andhence lowering the cost.

In certain embodiments, the spacers are deposited on the plates. Thedeposition can be evaporation, pasting, or a lift-off. In the pasting,the spacer is fabricated first on a carrier, then the spacer istransferred from the carrier to the plate. In the lift-off, a removablematerial is first deposited on the plate and holes are created in thematerial; the hole bottom expose the plate surface and then a spacermaterial is deposited into the hole and afterwards the removablematerial is removed, leaving only the spacers on the plate surface. Incertain embodiments, the spacers deposited on the plate are fused withthe plate. In certain embodiments, the spacer and the plates arefabricated in a single process. The single process includes imprinting(e.g. embossing, molding) or synthesis.

In certain embodiments, at least two of the spacers are fixed to therespective plate by different fabrication methods, and optionallywherein the different fabrication methods include at least one of beingdeposition, bonded, fuse, imprinted, and etched.

In certain embodiments, one or more of the spacers are fixed to therespective plate(s) is by a fabrication method of being bonded, beingfused, being imprinted, or being etched, or any combination of thereof.

In certain embodiments, the fabrication methods for forming suchmonolithic spacers on the plate include a method of being bonded, beingfused, being imprinted, or being etched, or any combination of thereof.

B) Adaptor

Details of the Adaptor are described in detail in a variety ofpublications including International Application No. PCT/US2018/017504,which is hereby incorporated by reference herein for all purposes.

The present invention that is described herein address this problem byproviding a system comprising an optical adaptor and a smartphone. Theoptical adaptor device fits over a smartphone converting it into amicroscope which can take both fluorescent and bright-field images of asample. This system can be operated conveniently and reliably by acommon person at any location. The optical adaptor takes advantage ofthe existing resources of the smartphone, including camera, lightsource, processor and display screen, which provides a low-cost solutionlet the user to do bright-field and fluorescent microscopy.

In this invention, the optical adaptor device comprises a holder framefitting over the upper part of the smartphone and an optical boxattached to the holder having sample receptacle slot and illuminationoptics. In some references (U.S. Pat. No. 2016/029091 and U.S. Pat. No.2011/0292198), their optical adaptor design is a whole piece includingboth the clip-on mechanics parts to fit over the smartphone and thefunctional optics elements. This design has the problem that they needto redesign the whole-piece optical adaptor for each specific model ofsmartphone. But in this present invention, the optical adaptor isseparated into a holder frame only for fitting a smartphone and auniversal optical box containing all the functional parts. For thesmartphones with different dimensions, as long as the relative positionsof the camera and the light source are the same, only the holder frameneed to be redesigned, which will save a lot of cost of design andmanufacture.

The optical box of the optical adaptor comprises: a receptacle slotwhich receives and position the sample in a sample slide in the field ofview and focal range of the smartphone camera; a bright-fieldillumination optics for capturing bright-field microscopy images of asample; a fluorescent illumination optics for capturing fluorescentmicroscopy images of a sample; a lever to switch between bright-fieldillumination optics and fluorescent illumination optics by slidinginward and outward in the optical box.

The receptacle slot has a rubber door attached to it, which can fullycover the slot to prevent the ambient light getting into the optical boxto be collected by the camera. In U.S. Pat. 2016/0290916, the sampleslot is always exposed to the ambient light which won't cause too muchproblem because it only does bright-field microscopy. But the presentinvention can take the advantage of this rubber door when doingfluorescent microscopy because the ambient light would bring a lot ofnoise to the image sensor of the camera.

To capture good fluorescent microscopy image, it is desirable thatnearly no excitation light goes into the camera and only the fluorescentemitted by the sample is collected by the camera. For all commonsmartphones, however, the optical filter putting in front of the cameracannot block the undesired wavelength range of the light emitted fromthe light source of a smartphone very well due to the large divergenceangle of the beams emitted by the light source and the optical filternot working well for un-collimated beams. Collimation optics can bedesigned to collimated the beam emitted by the smartphone light sourceto address this issue, but this approach increase the size and cost ofthe adaptor. Instead, in this present invention, fluorescentillumination optics enables the excitation light to illuminate thesample partially from the waveguide inside the sample slide andpartially from the backside of the sample side in large obliqueincidence angle so that excitation light will nearly not be collected bythe camera to reduce the noise signal getting into the camera.

The bright-field illumination optics in the adaptor receive and turn thebeam emitted by the light source so as to back-illuminated the sample innormal incidence angle.

Typically, the optical box also comprises a lens mounted in it alignedwith the camera of the smartphone, which magnifies the images capturedby the camera. The images captured by the camera can be furtherprocessed by the processor of smartphone and outputs the analysis resulton the screen of smartphone.

To achieve both bright-field illumination and fluorescent illuminationoptics in a same optical adaptor, in this present invention, a slidablelever is used. The optical elements of the fluorescent illuminationoptics are mounted on the lever and when the lever fully slides into theoptical box, the fluorescent illumination optics elements block theoptical path of bright-field illumination optics and switch theillumination optics to fluorescent illumination optics. And when thelever slides out, the fluorescent illumination optics elements mountedon the lever move out of the optical path and switch the illuminationoptics to bright-field illumination optics. This lever design makes theoptical adaptor work in both bright-field and fluorescent illuminationmodes without the need for designing two different single-mode opticalboxes.

The lever comprises two planes at different planes at different heights.

In certain embodiments, two planes can be joined together with avertical bar and move together in or out of the optical box. In certainembodiments, two planes can be separated and each plane can moveindividually in or out of the optical box.

The upper lever plane comprises at least one optical element which canbe, but not limited to be an optical filter. The upper lever plane movesunder the light source and the preferred distance between the upperlever plane and the light source is in the range of 0 to 5 mm.

Part of the bottom lever plane is not parallel to the image plane. Andthe surface of the non-parallel part of the bottom lever plane hasmirror finish with high reflectivity larger than 95%. The non-parallelpart of the bottom lever plane moves under the light source and deflectsthe light emitted from the light source to back-illuminate the samplearea right under the camera. The preferred tilt angle of thenon-parallel part of the bottom lever plane is in the range of 45 degreeto 65 degree and the tilt angle is defined as the angle between thenon-parallel bottom plane and the vertical plane.

Part of the bottom lever plane is parallel to the image plane and islocated under and 1 mm to 10 mm away from the sample. The surface of theparallel part of the bottom lever plane is highly light absorptive withlight absorption larger than 95%. This absorptive surface is toeliminate the reflective light back-illuminating on the sample in smallincidence angle.

To slide in and out to switch the illumination optics using the lever, astopper design comprising a ball plunger and a groove on the lever isused in order to stop the lever at a pre-defined position when beingpulled outward from the adaptor. This allow the user to use arbitraryforce the pull the lever but make the lever to stop at a fixed positionwhere the optical adaptor's working mode is switched to bright-filedillumination.

A sample slider is mounted inside the receptacle slot to receive theQMAX device and position the sample in the QMAX device in the field ofview and focal range of the smartphone camera.

The sample slider comprises a fixed track frame and a moveable arm:

The frame track is fixedly mounted in the receptacle slot of the opticalbox. And the track frame has a sliding track slot that fits the widthand thickness of the QMAX device so that the QMAX device can slide alongthe track. The width and height of the track slot is carefullyconfigured to make the QMAX device shift less than 0.5 mm in thedirection perpendicular to the sliding direction in the sliding planeand shift less than less than 0.2 mm along the thickness direction ofthe QMAX device.

The frame track has an opened window under the field of view of thecamera of smartphone to allow the light back-illuminate the sample.

A moveable arm is pre-built in the sliding track slot of the track frameand moves together with the QMAX device to guide the movement of QMAXdevice in the track frame.

The moveable arm equipped with a stopping mechanism with two pre-definedstop positions. For one position, the arm will make the QMAX device stopat the position where a fixed sample area on the QMAX device is rightunder the camera of smartphone. For the other position, the arm willmake the QMAX device stop at the position where the sample area on QMAXdevice is out of the field of view of the smartphone and the QMAX devicecan be easily taken out of the track slot.

The moveable arm switches between the two stop positions by a pressingthe QMAX device and the moveable arm together to the end of the trackslot and then releasing.

The moveable arm can indicate if the QMAX device is inserted in correctdirection. The shape of one corner of the QMAX device is configured tobe different from the other three right angle corners. And the shape ofthe moveable arm matches the shape of the corner with the special shapeso that only in correct direction can QMAX device slide to correctposition in the track slot.

C) Smartphone/Detection System

Details of the Smartphone/Detection System are described in detail in avariety of publications including International Application (IA) No.PCT/US2016/046437 filed on Aug. 10, 2016, IA No. PCT/US2016/051775 filedSep. 14, 2016, U.S. Provisional Application No. 62/456,065, which wasfiled on Feb. 7, 2017, U.S. Provisional Application Nos. 62/456,287 and62/456,590, which were filed on Feb. 8, 2017, U.S. ProvisionalApplication No. 62/456,504, which was filed on Feb. 8, 2017, U.S.Provisional Application No. 62/459,544, which was filed on Feb. 15,2017, and U.S. Provisional Application Nos. 62/460,075 and 62/459,920,which were filed on Feb. 16, 2017, each of which are hereby incorporatedherein by reference in their entirety for all purposes.

The devices/apparatus, systems, and methods herein disclosed can includeor use Q-cards for sample detection, analysis, and quantification. Incertain embodiments, the Q-card is used together with an adaptor thatcan connect the Q-card with a smartphone detection system. In certainembodiments, the smartphone comprises a camera and/or an illuminationsource. In certain embodiments, the smartphone comprises a camera, whichcan be used to capture images or the sample when the sample ispositioned in the field of view of the camera (e.g. by an adaptor). Incertain embodiments, the camera includes one set of lenses (e.g. as iniPhone™ 6). In certain embodiments, the camera includes at least twosets of lenses (e.g. as in iPhone™ 7). In certain embodiments, thesmartphone comprises a camera, but the camera is not used for imagecapturing.

In certain embodiments, the smartphone comprises a light source such asbut not limited to LED (light emitting diode). In certain embodiments,the light source is used to provide illumination to the sample when thesample is positioned in the field of view of the camera (e.g. by anadaptor). In certain embodiments, the light from the light source isenhanced, magnified, altered, and/or optimized by optical components ofthe adaptor.

In certain embodiments, the smartphone comprises a processor that isconfigured to process the information from the sample. The smartphoneincludes software instructions that, when executed by the processor, canenhance, magnify, and/or optimize the signals (e.g. images) from thesample. The processor can include one or more hardware components, suchas a central processing unit (CPU), an application-specific integratedcircuit (ASIC), an application-specific instruction-set processor(ASIP), a graphics processing unit (GPU), a physics processing unit(PPU), a digital signal processor (DSP), a field-programmable gate array(FPGA), a programmable logic device (PLD), a controller, amicrocontroller unit, a reduced instruction-set computer (RISC), amicroprocessor, or the like, or any combination thereof.

In certain embodiments, the smartphone comprises a communication unit,which is configured and/or used to transmit data and/or images relatedto the sample to another device. Merely by way of example, thecommunication unit can use a cable network, a wireline network, anoptical fiber network, a telecommunications network, an intranet, theInternet, a local area network (LAN), a wide area network (WAN), awireless local area network (WLAN), a metropolitan area network (MAN), awide area network (WAN), a public telephone switched network (PSTN), aBluetooth network, a ZigBee network, a near field communication (NFC)network, or the like, or any combination thereof. In certainembodiments, the smartphone is an iPhone™, an Android™ phone, or aWindows™ phone.

D) Method of Manufacture

Details of the Method of Manufacture are described in detail in avariety of publications including International Application No.PCT/US2018/057873 filed Oct. 26, 2018, which is hereby incorporated byreference herein for all purposes.

Devices of the disclosure can be fabricated using techniques well knownin the art. The choice of fabrication technique will depend on thematerial used for the device and the size of the spacer array and/or thesize of the spacers. Exemplary materials for fabricating the devices ofthe invention include glass, silicon, steel, nickel, polymers, e.g.,poly(methylmethacrylate) (PMMA), polycarbonate, polystyrene,polyethylene, polyolefins, silicones (e.g., poly(dimethylsiloxane)),polypropylene, cis-polyisoprene (rubber), poly(vinyl chloride) (PVC),poly(vinyl acetate) (PVAc), polychloroprene (neoprene),polytetrafluoroethylene (Teflon), poly(vinylidene chloride) (SaranA),and cyclic olefin polymer (COP) and cyclic olefin copolymer (COC), andcombinations thereof. Other materials are known in the art. For example,deep Reactive Ion Etch (DRIE) is used to fabricate silicon-based deviceswith small gaps, small spacers and large aspect ratios (ratio of spacerheight to lateral dimension). Thermoforming (embossing, injectionmolding) of plastic devices can also be used, e.g., when the smallestlateral feature is >20 microns and the aspect ratio of these features is≤10.

Additional methods include photolithography (e.g., stereolithography orx-ray photolithography), molding, embossing, silicon micromachining, wetor dry chemical etching, milling, diamond cutting, LithographieGalvanoformung and Abformung (LIGA), and electroplating. For example,for glass, traditional silicon fabrication techniques ofphotolithography followed by wet (KOH) or dry etching (reactive ionetching with fluorine or other reactive gas) can be employed. Techniquessuch as laser micromachining can be adopted for plastic materials withhigh photon absorption efficiency. This technique is suitable for lowerthroughput fabrication because of the serial nature of the process. Formass-produced plastic devices, thermoplastic injection molding, andcompression molding can be suitable. Conventional thermoplasticinjection molding used for mass-fabrication of compact discs (whichpreserves fidelity of features in sub-microns) can also be employed tofabricate the devices of the invention. For example, the device featuresare replicated on a glass master by conventional photolithography. Theglass master is electroformed to yield a tough, thermal shock resistant,thermally conductive, hard mold. This mold serves as the master templatefor injection molding or compression molding the features into a plasticdevice. Depending on the plastic material used to fabricate the devicesand the requirements on optical quality and throughput of the finishedproduct, compression molding or injection molding can be chosen as themethod of manufacture. Compression molding (also called hot embossing orrelief imprinting) has the advantages of being compatible with highmolecular weight polymers, which are excellent for small structures andcan replicate high aspect ratio structures but has longer cycle times.Injection molding works well for low aspect ratio structures and is mostsuitable for low molecular weight polymers.

A device can be fabricated in one or more pieces that are thenassembled. Layers of a device can be bonded together by clamps,adhesives, heat, anodic bonding, or reactions between surface groups(e.g., wafer bonding). Alternatively, a device with channels or gaps inmore than one plane can be fabricated as a single piece, e.g., usingstereolithography or other three-dimensional fabrication techniques.

To reduce non-specific adsorption of cells or compounds released bylysed cells onto the surfaces of the device, one or more surfaces of thedevice can be chemically modified to be non-adherent or repulsive. Thesurfaces can be coated with a thin film coating (e.g., a monolayer) ofcommercial non-stick reagents, such as those used to form hydrogels.Additional examples chemical species that can be used to modify thesurfaces of the device include oligoethylene glycols, fluorinatedpolymers, organosilanes, thiols, poly-ethylene glycol, hyaluronic acid,bovine serum albumin, poly-vinyl alcohol, mucin, poly-HEMA,methacrylated PEG, and agarose. Charged polymers can also be employed torepel oppositely charged species. The type of chemical species used forrepulsion and the method of attachment to the surfaces of the devicewill depend on the nature of the species being repelled and the natureof the surfaces and the species being attached. Such surfacemodification techniques are well known in the art. The surfaces can befunctionalized before or after the device is assembled. The surfaces ofthe device can also be coated in order to capture materials in thesample, e.g., membrane fragments or proteins.

In certain embodiments of the present disclosure, a method forfabricating any Q-Card of the present disclosure can comprise injectionmolding of the first plate. In certain embodiments of the presentdisclosure, a method for fabricating any Q-Card of the presentdisclosure can comprise nanoimprinting or extrusion printing of thesecond plate. In certain embodiments of the present disclosure, a methodfor fabricating any Q-Card of the present disclosure can comprise Lasercutting the first plate. In certain embodiments of the presentdisclosure, a method for fabricating any Q-Card of the presentdisclosure can comprise nanoimprinting or extrusion printing of thesecond plate. In certain embodiments of the present disclosure, a methodfor fabricating any Q-Card of the present disclosure can compriseinjection molding and laser cutting the first plate. In certainembodiments of the present disclosure, a method for fabricating anyQ-Card of the present disclosure can comprise nanoimprinting orextrusion printing of the second plate. In certain embodiments of thepresent disclosure, a method for fabricating any Q-Card of the presentdisclosure can comprise nanoimprinting or extrusion printing tofabricated both the first and the second plate. In certain embodimentsof the present disclosure, a method for fabricating any Q-Card of thepresent disclosure can comprise fabricating the first plate or thesecond plate, using injection molding, laser cutting the first plate,nanoimprinting, extrusion printing, or a combination of thereof. Incertain embodiments of the present disclosure, a method for fabricatingany Q-Card of the present disclosure can comprise a step of attachingthe hinge on the first and the second plates after the fabrication ofthe first and second plates.

E) Sample Types & Subjects

Details of the Samples & Subjects are described in detail in a varietyof publications including International Application (IA) No.PCT/US2016/046437 filed on Aug. 10, 2016, IA No. PCT/US2016/051775 filedon Sep. 14, 2016, IA No. PCT/US201/017307 filed on Feb. 7, 2018, IA No.and PCT/US2017/065440 filed on Dec. 8, 2017, each of which is herebyincorporated by reference herein for all purposes.

A sample can be obtained from a subject. A subject as described hereincan be of any age and can be an adult, infant or child. In some cases,the subject is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 years old, or within arange therein (e.g., between 2 and years old, between 20 and 40 yearsold, or between 40 and 90 years old). A particular class of subjectsthat can benefit is subjects who have or are suspected of having aninfection (e.g., a bacterial and/or a viral infection). Anotherparticular class of subjects that can benefit is subjects who can be athigher risk of getting an infection. Furthermore, a subject treated byany of the methods or compositions described herein can be male orfemale. Any of the methods, devices, or kits disclosed herein can alsobe performed on a non-human subject, such as a laboratory or farmanimal. Non-limiting examples of a non-human subjects include a dog, agoat, a guinea pig, a hamster, a mouse, a pig, a non-human primate(e.g., a gorilla, an ape, an orangutan, a lemur, or a baboon), a rat, asheep, a cow, or a zebrafish.

The devices, apparatus, systems, and methods herein disclosed can beused for samples such as but not limited to diagnostic samples, clinicalsamples, environmental samples and foodstuff samples.

For example, in certain embodiments, the devices, apparatus, systems,and methods herein disclosed are used for a sample that includes cells,tissues, bodily fluids and/or a mixture thereof. In certain embodiments,the sample comprises a human body fluid. In certain embodiments, thesample comprises at least one of cells, tissues, bodily fluids, stool,amniotic fluid, aqueous humour, vitreous humour, blood, whole blood,fractionated blood, plasma, serum, breast milk, cerebrospinal fluid,cerumen, chyle, chime, endolymph, perilymph, feces, gastric acid,gastric juice, lymph, mucus, nasal drainage, phlegm, pericardial fluid,peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum, semen,sputum, sweat, synovial fluid, tears, vomit, urine, and exhaled breathcondensate.

In certain embodiments, the devices, apparatus, systems, and methodsherein disclosed are used for an environmental sample that is obtainedfrom any suitable source, such as but not limited to: river, lake, pond,ocean, glaciers, icebergs, rain, snow, sewage, reservoirs, tap water,drinking water, etc.; solid samples from soil, compost, sand, rocks,concrete, wood, brick, sewage, etc.; and gaseous samples from the air,underwater heat vents, industrial exhaust, vehicular exhaust, etc. Incertain embodiments, the environmental sample is fresh from the source;in certain embodiments, the environmental sample is processed. Forexample, samples that are not in liquid form are converted to liquidform before the subject devices, apparatus, systems, and methods areapplied.

In certain embodiments, the devices, apparatus, systems, and methodsherein disclosed are used for a foodstuff sample, which is suitable orhas the potential to become suitable for animal consumption, e.g., humanconsumption. In certain embodiments, a foodstuff sample includes rawingredients, cooked or processed food, plant and animal sources of food,preprocessed food as well as partially or fully processed food, etc. Incertain embodiments, samples that are not in liquid form are convertedto liquid form before the subject devices, apparatus, systems, andmethods are applied.

The subject devices, apparatus, systems, and methods can be used toanalyze any volume of the sample. Examples of the volumes include, butare not limited to, about 10 mL or less, 5 mL or less, 3 mL or less, 1microliter (uL, also “uL” herein) or less, 500 uL or less, 300 uL orless, 250 uL or less, 200 uL or less, 170 uL or less, 150 uL or less,125 uL or less, 100 uL or less, 75 uL or less, 50 uL or less, 25 uL orless, 20 uL or less, 15 uL or less, 10 uL or less, 5 uL or less, 3 uL orless, 1 uL or less, 0.5 uL or less, 0.1 uL or less, 0.05 uL or less,0.001 uL or less, 0.0005 uL or less, 0.0001 uL or less, 10 pL or less, 1pL or less, or a range between any two of the values.

In certain embodiments, the volume of the sample includes, but is notlimited to, about 100 uL or less, 75 uL or less, 50 uL or less, 25 uL orless, 20 uL or less, 15 uL or less, 10 uL or less, 5 uL or less, 3 uL orless, 1 uL or less, 0.5 uL or less, 0.1 uL or less, 0.05 uL or less,0.001 uL or less, 0.0005 uL or less, 0.0001 uL or less, 10 pL or less, 1pL or less, or a range between any two of the values. In certainembodiments, the volume of the sample includes, but is not limited to,about 10 uL or less, 5 uL or less, 3 uL or less, 1 uL or less, 0.5 uL orless, 0.1 uL or less, 0.05 uL or less, 0.001 uL or less, 0.0005 uL orless, 0.0001 uL or less, 10 pL or less, 1 pL or less, or a range betweenany two of the values.

In certain embodiments, the amount of the sample is about a drop ofliquid. In certain embodiments, the amount of sample is the amountcollected from a pricked finger or fingerstick. In certain embodiments,the amount of sample is the amount collected from a microneedle,micropipette or a venous draw.

F) Machine Learning

Details of the Network are described in detail in a variety ofpublications including International Application (IA) No.PCT/US2018/017504 filed Feb. 8, 2018, and PCT/US2018/057877 filed Oct.26, 2018, each of which are hereby incorporated by reference herein forall purposes.

One aspect of the present invention provides a framework of machinelearning and deep learning for analyte detection and localization. Amachine learning algorithm is an algorithm that is able to learn fromdata. A more rigorous definition of machine learning is “A computerprogram is said to learn from experience E with respect to some class oftasks T and performance measure P, if its performance at tasks in T, asmeasured by P, improves with experience E.” It explores the study andconstruction of algorithms that can learn from and make predictions ondata—such algorithms overcome the static program instructions by makingdata driven predictions or decisions, through building a model fromsample inputs.

Deep learning is a specific kind of machine learning based on a set ofalgorithms that attempt to model high level abstractions in data. In asimple case, there might be two sets of neurons: ones that receive aninput signal and ones that send an output signal. When the input layerreceives an input, it passes on a modified version of the input to thenext layer. In a deep network, there are many layers between the inputand output (and the layers are not made of neurons but it can help tothink of it that way), allowing the algorithm to use multiple processinglayers, composed of multiple linear and non-linear transformations.

One aspect of the present invention is to provide two analyte detectionand localization approaches. The first approach is a deep learningapproach and the second approach is a combination of deep learning andcomputer vision approaches.

(i) Deep Learning Approach.

In the first approach, the disclosed analyte detection and localizationworkflow consists of two stages, training and prediction. We describetraining and prediction stages in the following paragraphs.

(a) Training Stage

In the training stage, training data with annotation is fed into aconvolutional neural network. Convolutional neural network is aspecialized neural network for processing data that has a grid-like,feed forward and layered network topology. Examples of the data includetime-series data, which can be thought of as a 1D grid taking samples atregular time intervals, and image data, which can be thought of as a 2Dgrid of pixels. Convolutional networks have been successful in practicalapplications. The name “convolutional neural network” indicates that thenetwork employs a mathematical operation called convolution. Convolutionis a specialized kind of linear operation. Convolutional networks aresimply neural networks that use convolution in place of general matrixmultiplication in at least one of their layers.

The machine learning model receives one or multiple images of samplesthat contain the analytes taken by the imager over the sample holdingQMAX device as training data. Training data are annotated for analytesto be assayed, wherein the annotations indicate whether or not analytesare in the training data and where they locate in the image. Annotationcan be done in the form of tight bounding boxes which fully contains theanalyte, or center locations of analytes. In the latter case, centerlocations are further converted into circles covering analytes or aGaussian kernel in a point map.

When the size of training data is large, training machine learning modelpresents two challenges: annotation (usually done by human) is timeconsuming, and the training is computationally expensive. To overcomethese challenges, one can partition the training data into patches ofsmall size, then annotate and train on these patches, or a portion ofthese patches. The term “machine learning” can refer to algorithms,systems and apparatus in the field of artificial intelligence that oftenuse statistical techniques and artificial neural network trained fromdata without being explicitly programmed.

The annotated images are fed to the machine learning (ML) trainingmodule, and the model trainer in the machine learning module will traina ML model from the training data (annotated sample images). The inputdata will be fed to the model trainer in multiple iterations untilcertain stopping criterion is satisfied. The output of the ML trainingmodule is a ML model—a computational model that is built from a trainingprocess in the machine learning from the data that gives computer thecapability to perform certain tasks (e.g. detect and classify theobjects) on its own.

The trained machine learning model is applied during the predication (orinference) stage by the computer. Examples of machine learning modelsinclude ResNet, DenseNet, etc. which are also named as “deep learningmodels” because of the depth of the connected layers in their networkstructure. In certain embodiments, the Caffe library with fullyconvolutional network (FCN) was used for model training and predication,and other convolutional neural network architecture and library can alsobe used, such as TensorFlow.

The training stage generates a model that will be used in the predictionstage. The model can be repeatedly used in the prediction stage forassaying the input. Thus, the computing unit only needs access to thegenerated model. It does not need access to the training data, norrequiring the training stage to be run again on the computing unit.

(b) Prediction Stage

In the predication/inference stage, a detection component is applied tothe input image, and an input image is fed into the predication(inference) module preloaded with a trained model generated from thetraining stage. The output of the prediction stage can be bounding boxesthat contain the detected analytes with their center locations or apoint map indicating the location of each analyte, or a heatmap thatcontains the information of the detected analytes.

When the output of the prediction stage is a list of bounding boxes, thenumber of analytes in the image of the sample for assaying ischaracterized by the number of detected bounding boxes. When the outputof the prediction stage is a point map, the number of analytes in theimage of the sample for assaying is characterized by the integration ofthe point map. When the output of the prediction is a heatmap, alocalization component is used to identify the location and the numberof detected analytes is characterized by the entries of the heatmap.

One embodiment of the localization algorithm is to sort the heatmapvalues into a one-dimensional ordered list, from the highest value tothe lowest value. Then pick the pixel with the highest value, remove thepixel from the list, along with its neighbors. Iterate the process topick the pixel with the highest value in the list, until all pixels areremoved from the list.

In the detection component using heatmap, an input image, along with themodel generated from the training stage, is fed into a convolutionalneural network, and the output of the detection stage is a pixel-levelprediction, in the form of a heatmap. The heatmap can have the same sizeas the input image, or it can be a scaled down version of the inputimage, and it is the input to the localization component. We disclose analgorithm to localize the analyte center. The main idea is toiteratively detect local peaks from the heatmap. After the peak islocalized, we calculate the local area surrounding the peak but withsmaller value. We remove this region from the heatmap and find the nextpeak from the remaining pixels. The process is repeated only all pixelsare removed from the heatmap.

In certain embodiments, the present invention provides the localizationalgorithm to sort the heatmap values into a one-dimensional orderedlist, from the highest value to the lowest value. Then pick the pixelwith the highest value, remove the pixel from the list, along with itsneighbors. Iterate the process to pick the pixel with the highest valuein the list, until all pixels are removed from the list.

Algorithm GlobalSearch (heatmap) Input:  heatmap Output:  loci loci ←{ }sort(heatmap) while (heatmap is not empty) {  s ← pop(heatmap)  D ←{disk center as s with radius R}  heatmap = heatmap \ D // remove D fromthe heatmap  add s to loci }

After sorting, heatmap is a one-dimensional ordered list, where theheatmap value is ordered from the highest to the lowest. Each heatmapvalue is associated with its corresponding pixel coordinates. The firstitem in the heatmap is the one with the highest value, which is theoutput of the pop(heatmap) function. One disk is created, where thecenter is the pixel coordinate of the one with highest heatmap value.Then all heatmap values whose pixel coordinates resides inside the diskis removed from the heatmap. The algorithm repeatedly pops up thehighest value in the current heatmap, removes the disk around it, tillthe items are removed from the heatmap.

In the ordered list heatmap, each item has the knowledge of theproceeding item, and the following item. When removing an item from theordered list, we make the following changes:

-   -   Assume the removing item is x_(r), its proceeding item is x_(p),        and its following item is x_(f).    -   For the proceeding item x_(p), re-define its following item to        the following item of the removing item. Thus, the following        item of x_(p) is now x_(f).    -   For the removing item x_(r), un-define its proceeding item and        following item, which removes it from the ordered list.    -   For the following item x_(f), re-define its proceeding item to        the proceeding item of the removed item. Thus, the proceeding        item of x_(f) is now x_(p).

After all items are removed from the ordered list, the localizationalgorithm is complete. The number of elements in the set loci will bethe count of analytes, and location information is the pixel coordinatefor each s in the set loci.

Another embodiment searches local peak, which is not necessary the onewith the highest heatmap value. To detect each local peak, we start froma random starting point, and search for the local maximal value. Afterwe find the peak, we calculate the local area surrounding the peak butwith smaller value. We remove this region from the heatmap and find thenext peak from the remaining pixels. The process is repeated only allpixels are removed from the heatmap.

Algorithm LocalSearch (s, heatmap) Input:  s: starting location (x, y) heatmap Output:  s: location of local peak. We only consider pixels ofvalue > 0. Algorithm Cover (s, heatmap) Input:  s: location of localpeak.  heatmap: Output:  cover: a set of pixels covered by peak:

This is a breadth-first-search algorithm starting from s, with onealtered condition of visiting points: a neighbor p of the currentlocation q is only added to cover if heatmap[p]>0 andheatmap[p]<=heatmap[q]. Therefore, each pixel in cover has anon-descending path leading to the local peak s.

Algorithm Localization (heatmap) Input:   heatmap Output:   loci loci ←{} pixels ←{all pixels from heatmap} while pixels is not empty {  s ←anypixel from pixels s ←LocalSearch(s, heatmap)   // s is now local peakprobe local region of radius R surrounding s for better local peak r ←Cover(s, heatmap) pixels ← pixels \ r      // remove all pixels in coveradd s to loci

(ii) Mixture of Deep Learning and Computer Vision Approaches.

In the second approach, the detection and localization are realized bycomputer vision algorithms, and a classification is realized by deeplearning algorithms, wherein the computer vision algorithms detect andlocate possible candidates of analytes, and the deep learning algorithmclassifies each possible candidate as a true analyte and false analyte.The location of all true analyte (along with the total count of trueanalytes) will be recorded as the output.

(a) Detection.

The computer vision algorithm detects possible candidate based on thecharacteristics of analytes, including but not limited to intensity,color, size, shape, distribution, etc. A pre-processing scheme canimprove the detection. Pre-processing schemes include contrastenhancement, histogram adjustment, color enhancement, de-nosing,smoothing, de-focus, etc. After pre-processing, the input image is sentto a detector. The detector tells the existing of possible candidate ofanalyte and gives an estimate of its location. The detection can bebased on the analyte structure (such as edge detection, line detection,circle detection, etc.), the connectivity (such as blob detection,connect components, contour detection, etc.), intensity, color, shapeusing schemes such as adaptive thresholding, etc.

(b) Localization.

After detection, the computer vision algorithm locates each possiblecandidate of analytes by providing its boundary or a tight bounding boxcontaining it. This can be achieved through object segmentationalgorithms, such as adaptive thresholding, background subtraction,floodfill, mean shift, watershed, etc. Very often, the localization canbe combined with detection to produce the detection results along withthe location of each possible candidates of analytes.

(c) Classification.

The deep learning algorithms, such as convolutional neural networks,achieve start-of-the-art visual classification. We employ deep learningalgorithms for classification on each possible candidate of analytes.Various convolutional neural network can be utilized for analyteclassification, such as VGGNet, ResNet, MobileNet, DenseNet, etc.

Given each possible candidate of analyte, the deep learning algorithmcomputes through layers of neurons via convolution filters andnon-linear filters to extract high-level features that differentiateanalyte against non-analytes. A layer of fully convolutional networkwill combine high-level features into classification results, whichtells whether it is a true analyte or not, or the probability of being aanalyte.

G) Applications, Bio/Chemical Biomarkers, and Health Conditions

The applications of the present invention include, but not limited to,(a) the detection, purification and quantification of chemical compoundsor biomolecules that correlates with the stage of certain diseases,e.g., infectious and parasitic disease, injuries, cardiovasculardisease, cancer, mental disorders, neuropsychiatric disorders andorganic diseases, e.g., pulmonary diseases, renal diseases, (b) thedetection, purification and quantification of microorganism, e.g.,virus, fungus and bacteria from environment, e.g., water, soil, orbiological samples, e.g., tissues, bodily fluids, (c) the detection,quantification of chemical compounds or biological samples that posehazard to food safety or national security, e.g. toxic waste, anthrax,(d) quantification of vital parameters in medical or physiologicalmonitor, e.g., glucose, blood oxygen level, total blood count, (e) thedetection and quantification of specific DNA or RNA from biosamples,e.g., cells, viruses, bodily fluids, (f) the sequencing and comparing ofgenetic sequences in DNA in the chromosomes and mitochondria for genomeanalysis or (g) to detect reaction products, e.g., during synthesis orpurification of pharmaceuticals.

The detection can be carried out in various sample matrix, such ascells, tissues, bodily fluids, and stool. Bodily fluids of interestinclude but are not limited to, amniotic fluid, aqueous humour, vitreoushumour, blood (e.g., whole blood, fractionated blood, plasma, serum,etc.), breast milk, cerebrospinal fluid (CSF), cerumen (earwax), chyle,chime, endolymph, perilymph, feces, gastric acid, gastric juice, lymph,mucus (including nasal drainage and phlegm), pericardial fluid,peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum (skin oil),semen, sputum, sweat, synovial fluid, tears, vomit, urine and exhaledcondensate. In certain embodiments, the sample comprises a human bodyfluid. In certain embodiments, the sample comprises at least one ofcells, tissues, bodily fluids, stool, amniotic fluid, aqueous humour,vitreous humour, blood, whole blood, fractionated blood, plasma, serum,breast milk, cerebrospinal fluid, cerumen, chyle, chime, endolymph,perilymph, feces, gastric acid, gastric juice, lymph, mucus, nasaldrainage, phlegm, pericardial fluid, peritoneal fluid, pleural fluid,pus, rheum, saliva, sebum, semen, sputum, sweat, synovial fluid, tears,vomit, urine, and exhaled condensate.

In embodiments, the sample is at least one of a biological sample, anenvironmental sample, and a biochemical sample.

The devices, systems and the methods in the present invention find usein a variety of different applications in various fields, wheredetermination of the presence or absence, and/or quantification of oneor more analytes in a sample are desired. For example, the subjectmethod finds use in the detection of proteins, peptides, nucleic acids,synthetic compounds, inorganic compounds, and the like. The variousfields include, but not limited to, human, veterinary, agriculture,foods, environments, drug testing, and others.

In certain embodiments, the subject method finds use in the detection ofnucleic acids, proteins, or other biomolecules in a sample. The methodscan include the detection of a set of biomarkers, e.g., two or moredistinct protein or nucleic acid biomarkers, in a sample. For example,the methods can be used in the rapid, clinical detection of two or moredisease biomarkers in a biological sample, e.g., as can be employed inthe diagnosis of a disease condition in a subject, or in the ongoingmanagement or treatment of a disease condition in a subject, etc. Asdescribed above, communication to a physician or other health-careprovider can better ensure that the physician or other health-careprovider is made aware of, and cognizant of, possible concerns and canthus be more likely to take appropriate action.

The applications of the devices, systems and methods in the presentinventions of employing a CROF device include, but are not limited to,(a) the detection, purification and quantification of chemical compoundsor biomolecules that correlates with the stage of certain diseases,e.g., infectious and parasitic disease, injuries, cardiovasculardisease, cancer, mental disorders, neuropsychiatric disorders andorganic diseases, e.g., pulmonary diseases, renal diseases, (b) thedetection, purification and quantification of microorganism, e.g.,virus, fungus and bacteria from environment, e.g., water, soil, orbiological samples, e.g., tissues, bodily fluids, (c) the detection,quantification of chemical compounds or biological samples that posehazard to food safety or national security, e.g. toxic waste, anthrax,(d) quantification of vital parameters in medical or physiologicalmonitor, e.g., glucose, blood oxygen level, total blood count, (e) thedetection and quantification of specific DNA or RNA from biosamples,e.g., cells, viruses, bodily fluids, (f) the sequencing and comparing ofgenetic sequences in DNA in the chromosomes and mitochondria for genomeanalysis or (g) to detect reaction products, e.g., during synthesis orpurification of pharmaceuticals. Some of the specific applications ofthe devices, systems and methods in the present invention are describednow in further detail.

The applications of the present invention include, but not limited to,(a) the detection, purification and quantification of chemical compoundsor biomolecules that correlates with the stage of certain diseases,e.g., infectious and parasitic disease, injuries, cardiovasculardisease, cancer, mental disorders, neuropsychiatric disorders andorganic diseases, e.g., pulmonary diseases, renal diseases, (b) thedetection, purification and quantification of microorganism, e.g.,virus, fungus and bacteria from environment, e.g., water, soil, orbiological samples, e.g., tissues, bodily fluids, (c) the detection,quantification of chemical compounds or biological samples that posehazard to food safety or national security, e.g. toxic waste, anthrax,(d) quantification of vital parameters in medical or physiologicalmonitor, e.g., glucose, blood oxygen level, total blood count, (e) thedetection and quantification of specific DNA or RNA from biosamples,e.g., cells, viruses, bodily fluids, (f) the sequencing and comparing ofgenetic sequences in DNA in the chromosomes and mitochondria for genomeanalysis or (g) to detect reaction products, e.g., during synthesis orpurification of pharmaceuticals.

An implementation of the devices, systems and methods in the presentinvention can include a) obtaining a sample, b) applying the sample toCROF device containing a capture agent that binds to an analyte ofinterest, under conditions suitable for binding of the analyte in asample to the capture agent, c) washing the CROF device, and d) readingthe CROF device, thereby obtaining a measurement of the amount of theanalyte in the sample. In certain embodiments, the analyte can be abiomarker, an environmental marker, or a foodstuff marker. The sample insome instances is a liquid sample, and can be a diagnostic sample (suchas saliva, serum, blood, sputum, urine, sweat, lacrima, semen, ormucus); an environmental sample obtained from a river, ocean, lake,rain, snow, sewage, sewage processing runoff, agricultural runoff,industrial runoff, tap water or drinking water; or a foodstuff sampleobtained from tap water, drinking water, prepared food, processed foodor raw food.

In any embodiment, the CROF device can be placed in a microfluidicdevice and the applying step b) can include applying a sample to amicrofluidic device comprising the CROF device.

In any embodiment, the reading step d) can include detecting afluorescence or luminescence signal from the CROF device.

In any embodiment, the reading step d) can include reading the CROFdevice with a handheld device configured to read the CROF device. Thehandheld device can be a mobile phone, e.g., a smart phone.

In any embodiment, the CROF device can include a labeling agent that canbind to an analyte-capture agent complex on the CROF device.

In any embodiment, the devices, systems and methods in the presentinvention can further include, between steps c) and d), the steps ofapplying to the CROF device a labeling agent that binds to ananalyte-capture agent complex on the CROF device, and washing the CROFdevice.

In any embodiment, the reading step d) can include reading an identifierfor the CROF device. The identifier can be an optical barcode, a radiofrequency ID tag, or combinations thereof.

In any embodiment, the devices, systems and methods in the presentinvention can further include applying a control sample to a controlCROF device containing a capture agent that binds to the analyte,wherein the control sample includes a known detectable amount of theanalyte, and reading the control CROF device, thereby obtaining acontrol measurement for the known detectable amount of the analyte in asample.

In any embodiment, the sample can be a diagnostic sample obtained from asubject, the analyte can be a biomarker, and the measured amount of theanalyte in the sample can be diagnostic of a disease or a condition.

In any embodiment, the devices, systems and methods in the presentinvention can further include receiving or providing to the subject areport that indicates the measured amount of the biomarker and a rangeof measured values for the biomarker in an individual free of or at lowrisk of having the disease or condition, wherein the measured amount ofthe biomarker relative to the range of measured values is diagnostic ofa disease or condition.

In any embodiment, the devices, systems and methods in the presentinvention can further include diagnosing the subject based oninformation including the measured amount of the biomarker in thesample. In some cases, the diagnosing step includes sending datacontaining the measured amount of the biomarker to a remote location andreceiving a diagnosis based on information including the measurementfrom the remote location.

In any embodiment, the applying step b) can include isolating miRNA fromthe sample to generate an isolated miRNA sample, and applying theisolated miRNA sample to the disk-coupled dots-on-pillar antenna (CROFdevice) array.

In any embodiment, the method can include receiving or providing areport that indicates the safety or harmfulness for a subject to beexposed to the environment from which the sample was obtained.

In any embodiment, the method can include sending data containing themeasured amount of the environmental marker to a remote location andreceiving a report that indicates the safety or harmfulness for asubject to be exposed to the environment from which the sample wasobtained.

In any embodiment, the CROF device array can include a plurality ofcapture agents that each binds to an environmental marker, and whereinthe reading step d) can include obtaining a measure of the amount of theplurality of environmental markers in the sample.

In any embodiment, the sample can be a foodstuff sample, wherein theanalyte can be a foodstuff marker, and wherein the amount of thefoodstuff marker in the sample can correlate with safety of thefoodstuff for consumption.

In any embodiment, the method can include receiving or providing areport that indicates the safety or harmfulness for a subject to consumethe foodstuff from which the sample is obtained.

In any embodiment, the method can include sending data containing themeasured amount of the foodstuff marker to a remote location andreceiving a report that indicates the safety or harmfulness for asubject to consume the foodstuff from which the sample is obtained.

In any embodiment, the CROF device array can include a plurality ofcapture agents that each binds to a foodstuff marker, wherein theobtaining can include obtaining a measure of the amount of the pluralityof foodstuff markers in the sample, and wherein the amount of theplurality of foodstuff marker in the sample can correlate with safety ofthe foodstuff for consumption.

Also provided herein are kits that find use in practicing the devices,systems and methods in the present invention.

The amount of sample can be about a drop of a sample. The amount ofsample can be the amount collected from a pricked finger or fingerstick.The amount of sample can be the amount collected from a microneedle or avenous draw.

A sample can be used without further processing after obtaining it fromthe source, or can be processed, e.g., to enrich for an analyte ofinterest, remove large particulate matter, dissolve or resuspend a solidsample, etc.

Any suitable method of applying a sample to the CROF device can beemployed. Suitable methods can include using a pipet, dropper, syringe,etc. In certain embodiments, when the CROF device is located on asupport in a dipstick format, as described below, the sample can beapplied to the CROF device by dipping a sample-receiving area of thedipstick into the sample.

A sample can be collected at one time, or at a plurality of times.Samples collected over time can be aggregated and/or processed (byapplying to a CROF device and obtaining a measurement of the amount ofanalyte in the sample, as described herein) individually. In someinstances, measurements obtained over time can be aggregated and can beuseful for longitudinal analysis over time to facilitate screening,diagnosis, treatment, and/or disease prevention.

Washing the CROF device to remove unbound sample components can be donein any convenient manner, as described above. In certain embodiments,the surface of the CROF device is washed using binding buffer to removeunbound sample components.

Detectable labeling of the analyte can be done by any convenient method.The analyte can be labeled directly or indirectly. In direct labeling,the analyte in the sample is labeled before the sample is applied to theCROF device. In indirect labeling, an unlabeled analyte in a sample islabeled after the sample is applied to the CROF device to capture theunlabeled analyte, as described below.

The samples from a subject, the health of a subject, and otherapplications of the present invention are further described below.Exemplary samples, health conditions, and application are also disclosedin, e.g., U.S. Pub. Nos. 2014/0154668 and 2014/0045209, which are herebyincorporated by reference.

The present inventions find use in a variety of applications, where suchapplications are generally analyte detection applications in which thepresence of a particular analyte in a given sample is detected at leastqualitatively, if not quantitatively. Protocols for carrying out analytedetection assays are well known to those of skill in the art and neednot be described in great detail here. Generally, the sample suspectedof comprising an analyte of interest is contacted with the surface of asubject nanosensor under conditions sufficient for the analyte to bindto its respective capture agent that is tethered to the sensor. Thecapture agent has highly specific affinity for the targeted molecules ofinterest. This affinity can be antigen-antibody reaction whereantibodies bind to specific epitope on the antigen, or a DNA/RNA orDNA/RNA hybridization reaction that is sequence-specific between two ormore complementary strands of nucleic acids. Thus, if the analyte ofinterest is present in the sample, it likely binds to the sensor at thesite of the capture agent and a complex is formed on the sensor surface.Namely, the captured analytes are immobilized at the sensor surface.After removing the unbounded analytes, the presence of this bindingcomplex on the surface of the sensor (e.g. the immobilized analytes ofinterest) is then detected, e.g., using a labeled secondary captureagent.

Specific analyte detection applications of interest includehybridization assays in which the nucleic acid capture agents areemployed and protein binding assays in which polypeptides, e.g.,antibodies, are employed. In these assays, a sample is first preparedand following sample preparation, the sample is contacted with a subjectnanosensor under specific binding conditions, whereby complexes areformed between target nucleic acids or polypeptides (or other molecules)that are complementary to capture agents attached to the sensor surface.

In one embodiment, the capture oligonucleotide is synthesized singlestrand DNA of 20-100 bases length, that is thiolated at one end. Thesemolecules are immobilized on the nanodevices' surface to capture thetargeted single-strand DNA (which can be at least 50 bp length) that hasa sequence that is complementary to the immobilized capture DNA. Afterthe hybridization reaction, a detection single strand DNA (which can beof 20-100 bp in length) whose sequence are complementary to the targetedDNA's unoccupied nucleic acid is added to hybridize with the target. Thedetection DNA has its one end conjugated to a fluorescence label, whoseemission wavelength are within the plasmonic resonance of thenanodevice. Therefore by detecting the fluorescence emission emanatefrom the nanodevices' surface, the targeted single strand DNA can beaccurately detected and quantified. The length for capture and detectionDNA determine the melting temperature (nucleotide strands will separateabove melting temperature), the extent of misparing (the longer thestrand, the lower the misparing).

One of the concerns of choosing the length for complementary bindingdepends on the needs to minimize misparing while keeping the meltingtemperature as high as possible. In addition, the total length of thehybridization length is determined in order to achieve optimum signalamplification.

A subject sensor can be employed in a method of diagnosing a disease orcondition, comprising: (a) obtaining a liquid sample from a patientsuspected of having the disease or condition, (b) contacting the samplewith a subject nanosensor, wherein the capture agent of the nanosensorspecifically binds to a biomarker for the disease and wherein thecontacting is done under conditions suitable for specific binding of thebiomarker with the capture agent; (c) removing any biomarker that is notbound to the capture agent; and (d) reading a light signal frombiomarker that remain bound to the nanosensor, wherein a light signalindicates that the patient has the disease or condition, wherein themethod further comprises labeling the biomarker with a light-emittinglabel, either prior to or after it is bound to the capture agent. Aswill be described in greater detail below, the patient can suspected ofhaving cancer and the antibody binds to a cancer biomarker. In otherembodiments, the patient is suspected of having a neurological disorderand the antibody binds to a biomarker for the neurological disorder.

The applications of the subject sensor include, but not limited to, (a)the detection, purification and quantification of chemical compounds orbiomolecules that correlates with the stage of certain diseases, e.g.,infectious and parasitic disease, injuries, cardiovascular disease,cancer, mental disorders, neuropsychiatric disorders and organicdiseases, e.g., pulmonary diseases, renal diseases, (b) the detection,purification and quantification of microorganism, e.g., virus, fungusand bacteria from environment, e.g., water, soil, or biological samples,e.g., tissues, bodily fluids, (c) the detection, quantification ofchemical compounds or biological samples that pose hazard to food safetyor national security, e.g. toxic waste, anthrax, (d) quantification ofvital parameters in medical or physiological monitor, e.g., glucose,blood oxygen level, total blood count, (e) the detection andquantification of specific DNA or RNA from biosamples, e.g., cells,viruses, bodily fluids, (f) the sequencing and comparing of geneticsequences in DNA in the chromosomes and mitochondria for genome analysisor (g) to detect reaction products, e.g., during synthesis orpurification of pharmaceuticals.

The detection can be carried out in various sample matrix, such ascells, tissues, bodily fluids, and stool. Bodily fluids of interestinclude but are not limited to, amniotic fluid, aqueous humour, vitreoushumour, blood (e.g., whole blood, fractionated blood, plasma, serum,etc.), breast milk, cerebrospinal fluid (CSF), cerumen (earwax), chyle,chime, endolymph, perilymph, feces, gastric acid, gastric juice, lymph,mucus (including nasal drainage and phlegm), pericardial fluid,peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum (skin oil),semen, sputum, sweat, synovial fluid, tears, vomit, urine and exhaledcondensate.

In certain embodiments, a subject biosensor can be used diagnose apathogen infection by detecting a target nucleic acid from a pathogen ina sample. The target nucleic acid can be, for example, from a virus thatis selected from the group comprising human immunodeficiency virus 1 and2 (HIV-1 and HIV-2), human T-cell leukaemia virus and 2 (HTLV-1 andHTLV-2), respiratory syncytial virus (RSV), adenovirus, hepatitis Bvirus (HBV), hepatitis C virus (HCV), Epstein-Barr virus (EBV), humanpapillomavirus (HPV), varicella zoster virus (VZV), cytomegalovirus(CMV), herpes-simplex virus 1 and 2 (HSV-1 and HSV-2), human herpesvirus8 (HHV-8, also known as Kaposi sarcoma herpesvirus) and flaviviruses,including yellow fever virus, dengue virus, Japanese encephalitis virus,West Nile virus and Ebola virus. The present invention is not, however,limited to the detection of nucleic acid, e.g., DNA or RNA, sequencesfrom the aforementioned viruses, but can be applied without any problemto other pathogens important in veterinary and/or human medicine.

Human papillomaviruses (HPV) are further subdivided on the basis oftheir DNA sequence homology into more than 70 different types. Thesetypes cause different diseases. HPV types 1, 2, 3, 4, 7, 10 and 26-29cause benign warts. HPV types 5, 8, 9, 12, 14, 15, 17 and 19-25 and46-50 cause lesions in patients with a weakened immune system. Types 6,11, 34, 39, 41-44 and 51-55 cause benign acuminate warts on the mucosaeof the genital region and of the respiratory tract. HPV types 16 and 18are of special medical interest, as they cause epithelial dysplasias ofthe genital mucosa and are associated with a high proportion of theinvasive carcinomas of the cervix, vagina, vulva and anal canal.Integration of the DNA of the human papillomavirus is considered to bedecisive in the carcinogenesis of cervical cancer. Humanpapillomaviruses can be detected for example from the DNA sequence oftheir capsid proteins L1 and L2. Accordingly, the method of the presentinvention is especially suitable for the detection of DNA sequences ofHPV types 16 and/or 18 in tissue samples, for assessing the risk ofdevelopment of carcinoma.

In some cases, the nanosensor can be employed to detect a biomarker thatis present at a low concentration. For example, the nanosensor can beused to detect cancer antigens in a readily accessible bodily fluids(e.g., blood, saliva, urine, tears, etc.), to detect biomarkers fortissue-specific diseases in a readily accessible bodily fluid (e.g., abiomarkers for a neurological disorder (e.g., Alzheimer's antigens)), todetect infections (particularly detection of low titer latent viruses,e.g., HIV), to detect fetal antigens in maternal blood, and fordetection of exogenous compounds (e.g., drugs or pollutants) in asubject's bloodstream, for example.

The following table provides a list of protein biomarkers that can bedetected using the subject nanosensor (when used in conjunction with anappropriate monoclonal antibody), and their associated diseases. Onepotential source of the biomarker (e.g., “CSF”; cerebrospinal fluid) isalso indicated in the table. In many cases, the subject biosensor candetect those biomarkers in a different bodily fluid to that indicated.For example, biomarkers that are found in CSF can be identified inurine, blood or saliva.

H) Utility

The subject method finds use in a variety of different applicationswhere determination of the presence or absence, and/or quantification ofone or more analytes in a sample are desired. For example, the subjectmethod finds use in the detection of proteins, peptides, nucleic acids,synthetic compounds, inorganic compounds, and the like.

In certain embodiments, the subject method finds use in the detection ofnucleic acids, proteins, or other biomolecules in a sample. The methodscan include the detection of a set of biomarkers, e.g., two or moredistinct protein or nucleic acid biomarkers, in a sample. For example,the methods can be used in the rapid, clinical detection of two or moredisease biomarkers in a biological sample, e.g., as can be employed inthe diagnosis of a disease condition in a subject, or in the ongoingmanagement or treatment of a disease condition in a subject, etc. Asdescribed above, communication to a physician or other health-careprovider can better ensure that the physician or other health-careprovider is made aware of, and cognizant of, possible concerns and canthus be more likely to take appropriate action.

The applications of the devices, systems and methods in the presentinvention of employing a CROF device include, but are not limited to,(a) the detection, purification and quantification of chemical compoundsor biomolecules that correlates with the stage of certain diseases,e.g., infectious and parasitic disease, injuries, cardiovasculardisease, cancer, mental disorders, neuropsychiatric disorders andorganic diseases, e.g., pulmonary diseases, renal diseases, (b) thedetection, purification and quantification of microorganism, e.g.,virus, fungus and bacteria from environment, e.g., water, soil, orbiological samples, e.g., tissues, bodily fluids, (c) the detection,quantification of chemical compounds or biological samples that posehazard to food safety or national security, e.g. toxic waste, anthrax,(d) quantification of vital parameters in medical or physiologicalmonitor, e.g., glucose, blood oxygen level, total blood count, (e) thedetection and quantification of specific DNA or RNA from biosamples,e.g., cells, viruses, bodily fluids, (f) the sequencing and comparing ofgenetic sequences in DNA in the chromosomes and mitochondria for genomeanalysis or (g) to detect reaction products, e.g., during synthesis orpurification of pharmaceuticals. Some of the specific applications ofthe devices, systems and methods in the present invention are describednow in further detail.

I) Diagnostic Method

In certain embodiments, the subject method finds use in detectingbiomarkers. In certain embodiments, the devices, systems and methods inthe present invention of using CROF are used to detect the presence orabsence of particular biomarkers, as well as an increase or decrease inthe concentration of particular biomarkers in blood, plasma, serum, orother bodily fluids or excretions, such as but not limited to urine,blood, serum, plasma, saliva, semen, prostatic fluid, nipple aspiratefluid, lachrymal fluid, perspiration, feces, cheek swabs, cerebrospinalfluid, cell lysate samples, amniotic fluid, gastrointestinal fluid,biopsy tissue, and the like. Thus, the sample, e.g. a diagnostic sample,can include various fluid or solid samples.

In some instances, the sample can be a bodily fluid sample from asubject who is to be diagnosed. In some instances, solid or semi-solidsamples can be provided. The sample can include tissues and/or cellscollected from the subject. The sample can be a biological sample.Examples of biological samples can include but are not limited to,blood, serum, plasma, a nasal swab, a nasopharyngeal wash, saliva,urine, gastric fluid, spinal fluid, tears, stool, mucus, sweat, earwax,oil, a glandular secretion, cerebral spinal fluid, tissue, semen,vaginal fluid, interstitial fluids derived from tumorous tissue, ocularfluids, spinal fluid, a throat swab, breath, hair, finger nails, skin,biopsy, placental fluid, amniotic fluid, cord blood, lymphatic fluids,cavity fluids, sputum, pus, microbiota, meconium, breast milk, exhaledcondensate and/or other excretions. The samples can includenasopharyngeal wash. Nasal swabs, throat swabs, stool samples, hair,finger nail, ear wax, breath, and other solid, semi-solid, or gaseoussamples can be processed in an extraction buffer, e.g., for a fixed orvariable amount of time, prior to their analysis. The extraction bufferor an aliquot thereof can then be processed similarly to other fluidsamples if desired. Examples of tissue samples of the subject caninclude but are not limited to, connective tissue, muscle tissue,nervous tissue, epithelial tissue, cartilage, cancerous sample, or bone.

In some instances, the subject from which a diagnostic sample isobtained can be a healthy individual, or can be an individual at leastsuspected of having a disease or a health condition. In some instances,the subject can be a patient.

In certain embodiments, the CROF device includes a capture agentconfigured to specifically bind a biomarker in a sample provided by thesubject. In certain embodiments, the biomarker can be a protein. Incertain embodiments, the biomarker protein is specifically bound by anantibody capture agent present in the CROF device. In certainembodiments, the biomarker is an antibody specifically bound by anantigen capture agent present in the CROF device. In certainembodiments, the biomarker is a nucleic acid specifically bound by anucleic acid capture agent that is complementary to one or both strandsof a double-stranded nucleic acid biomarker, or complementary to asingle-stranded biomarker. In certain embodiments, the biomarker is anucleic acid specifically bound by a nucleic acid binding protein. Incertain embodiments, the biomarker is specifically bound by an aptamer.

The presence or absence of a biomarker or significant changes in theconcentration of a biomarker can be used to diagnose disease risk,presence of disease in an individual, or to tailor treatments for thedisease in an individual. For example, the presence of a particularbiomarker or panel of biomarkers can influence the choices of drugtreatment or administration regimes given to an individual. Inevaluating potential drug therapies, a biomarker can be used as asurrogate for a natural endpoint such as survival or irreversiblemorbidity. If a treatment alters the biomarker, which has a directconnection to improved health, the biomarker can serve as a surrogateendpoint for evaluating the clinical benefit of a particular treatmentor administration regime. Thus, personalized diagnosis and treatmentbased on the particular biomarkers or panel of biomarkers detected in anindividual are facilitated by the subject method. Furthermore, the earlydetection of biomarkers associated with diseases is facilitated by thehigh sensitivity of the devices, systems and methods in the presentinvention, as described above. Due to the capability of detectingmultiple biomarkers with a mobile device, such as a smartphone, combinedwith sensitivity, scalability, and ease of use, the presently disclosedmethod finds use in portable and point-of-care or near-patient moleculardiagnostics.

In certain embodiments, the subject method finds use in detectingbiomarkers for a disease or disease state. In certain instances, thesubject method finds use in detecting biomarkers for thecharacterization of cell signaling pathways and intracellularcommunication for drug discovery and vaccine development. For example,the subject method can be used to detect and/or quantify the amount ofbiomarkers in diseased, healthy or benign samples. In certainembodiments, the subject method finds use in detecting biomarkers for aninfectious disease or disease state. In some cases, the biomarkers canbe molecular biomarkers, such as but not limited to proteins, nucleicacids, carbohydrates, small molecules, and the like.

The subject method find use in diagnostic assays, such as, but notlimited to, the following: detecting and/or quantifying biomarkers, asdescribed above; screening assays, where samples are tested at regularintervals for asymptomatic subjects; prognostic assays, where thepresence and or quantity of a biomarker is used to predict a likelydisease course; stratification assays, where a subject's response todifferent drug treatments can be predicted; efficacy assays, where theefficacy of a drug treatment is monitored; and the like.

In certain embodiments, a subject biosensor can be used diagnose apathogen infection by detecting a target nucleic acid from a pathogen ina sample. The target nucleic acid can be, for example, from a virus thatis selected from the group comprising human immunodeficiency virus 1 and2 (HIV-1 and HIV-2), human T-cell leukaemia virus and 2 (HTLV-1 andHTLV-2), respiratory syncytial virus (RSV), adenovirus, hepatitis Bvirus (HBV), hepatitis C virus (HCV), Epstein-Barr virus (EBV), humanpapillomavirus (HPV), varicella zoster virus (VZV), cytomegalovirus(CMV), herpes-simplex virus 1 and 2 (HSV-1 and HSV-2), human herpesvirus8 (HHV-8, also known as Kaposi sarcoma herpesvirus) and flaviviruses,including yellow fever virus, dengue virus, Japanese encephalitis virus,West Nile virus and Ebola virus. The present invention is not, however,limited to the detection of nucleic acid, e.g., DNA or RNA, sequencesfrom the aforementioned viruses, but can be applied without any problemto other pathogens important in veterinary and/or human medicine.

Human papillomaviruses (HPV) are further subdivided on the basis oftheir DNA sequence homology into more than 70 different types. Thesetypes cause different diseases. HPV types 1, 2, 3, 4, 7, 10 and 26-29cause benign warts. HPV types 5, 8, 9, 12, 14, 15, 17 and 19-25 and46-50 cause lesions in patients with a weakened immune system. Types 6,11, 34, 39, 41-44 and 51-55 cause benign acuminate warts on the mucosaeof the genital region and of the respiratory tract. HPV types 16 and 18are of special medical interest, as they cause epithelial dysplasias ofthe genital mucosa and are associated with a high proportion of theinvasive carcinomas of the cervix, vagina, vulva and anal canal.Integration of the DNA of the human papillomavirus is considered to bedecisive in the carcinogenesis of cervical cancer. Humanpapillomaviruses can be detected for example from the DNA sequence oftheir capsid proteins L1 and L2. Accordingly, the method of the presentinvention is especially suitable for the detection of DNA sequences ofHPV types 16 and/or 18 in tissue samples, for assessing the risk ofdevelopment of carcinoma.

Other pathogens that can be detected in a diagnostic sample using thedevices, systems and methods in the present invention include, but arenot limited to: Varicella zoster, Staphylococcus epidermidis,Escherichia coli, methicillin-resistant Staphylococcus aureus (MSRA),Staphylococcus aureus, Staphylococcus hominis, Enterococcus faecalis,Pseudomonas aeruginosa, Staphylococcus capitis, Staphylococcus warneri,Klebsiella pneumoniae, Haemophilus influenzae, Staphylococcus simulans,Streptococcus pneumoniae and Candida albicans; gonorrhea (Neisseriagorrhoeae), syphilis (Treponena pallidum), clamydia (Clamydatracomitis), nongonococcal urethritis (Ureaplasm urealyticum), chancroid(Haemophilus ducreyi), trichomoniasis (Trichomonas vaginalis);Pseudomonas aeruginosa, methicillin-resistant Staphlococccus aureus(MSRA), Klebsiella pneumoniae, Haemophilis influenzae, Staphylococcusaureus, Stenotrophomonas maltophilia, Haemophilis parainfluenzae,Escherichia coli, Enterococcus faecalis, Serratia marcescens,Haemophilis parahaemolyticus, Enterococcus cloacae, Candida albicans,Moraxiella catarrhalis, Streptococcus pneumoniae, Citrobacter freundii,Enterococcus faecium, Klebsella oxytoca, Pseudomonas fluorscens,Neiseria meningitidis, Streptococcus pyogenes, Pneumocystis carinii,Klebsella pneumoniae Legionella pneumophila, Mycoplasma pneumoniae, andMycobacterium tuberculosis, etc.

In some cases, the CROF device can be employed to detect a biomarkerthat is present at a low concentration. For example, the CROF device canbe used to detect cancer antigens in a readily accessible bodily fluids(e.g., blood, saliva, urine, tears, etc.), to detect biomarkers fortissue-specific diseases in a readily accessible bodily fluid (e.g., abiomarkers for a neurological disorder (e.g., Alzheimer's antigens)), todetect infections (particularly detection of low titer latent viruses,e.g., HIV), to detect fetal antigens in maternal blood, and fordetection of exogenous compounds (e.g., drugs or pollutants) in asubject's bloodstream, for example.

One potential source of the biomarker (e.g., “CSF”; cerebrospinal fluid)is also indicated in the table. In many cases, the subject biosensor candetect those biomarkers in a different bodily fluid to that indicated.For example, biomarkers that are found in CSF can be identified inurine, blood or saliva. It will also be clear to one with ordinary skillin the art that the subject CROF devices can be configured to captureand detect many more biomarkers known in the art that are diagnostic ofa disease or health condition.

A biomarker can be a protein or a nucleic acid (e.g., mRNA) biomarker,unless specified otherwise. The diagnosis can be associated with anincrease or a decrease in the level of a biomarker in the sample, unlessspecified otherwise. Lists of biomarkers, the diseases that they can beused to diagnose, and the sample in which the biomarkers can be detectedare described in Tables 1 and 2 of U.S. provisional application Ser. No.62/234,538, filed on Sep. 29, 2015, which application is incorporated byreference herein.

In some instances, the devices, systems and methods in the presentinvention is used to inform the subject from whom the sample is derivedabout a health condition thereof. Health conditions that can bediagnosed or measured by the devices, systems and methods in the presentinvention, device and system include, but are not limited to: chemicalbalance; nutritional health; exercise; fatigue; sleep; stress;prediabetes; allergies; aging; exposure to environmental toxins,pesticides, herbicides, synthetic hormone analogs; pregnancy; menopause;and andropause. Table 3 of U.S. provisional application Ser. No.62/234,538, filed on Sep. 29, 2015, which application is incorporated byreference herein, provides a list of biomarker that can be detectedusing the present CROF device (when used in conjunction with anappropriate monoclonal antibody, nucleic acid, or other capture agent),and their associated health conditions.

J) Kits

Aspects of the present disclosure include a kit that find use inperforming the devices, systems and methods in the present invention, asdescribed above. In certain embodiments, the kit includes instructionsfor practicing the subject methods using a hand held device, e.g., amobile phone. These instructions can be present in the subject kits in avariety of forms, one or more of which can be present in the kit. Oneform in which these instructions can be present is as printedinformation on a suitable medium or substrate, e.g., a piece or piecesof paper on which the information is printed, in the packaging of thekit, in a package insert, etc. Another means would be a computerreadable medium, e.g., diskette, CD, DVD, Blu-Ray, computer-readablememory, etc., on which the information has been recorded or stored. Yetanother means that can be present is a website address which can be usedvia the Internet to access the information at a removed site. The kitcan further include a software for implementing a method for measuringan analyte on a device, as described herein, provided on a computerreadable medium. Any convenient means can be present in the kits.

In certain embodiments, the kit includes a detection agent that includesa detectable label, e.g. a fluorescently labeled antibody oroligonucleotide that binds specifically to an analyte of interest, foruse in labeling the analyte of interest. The detection agent can beprovided in a separate container as the CROF device, or can be providedin the CROF device.

In certain embodiments, the kit includes a control sample that includesa known detectable amount of an analyte that is to be detected in thesample. The control sample can be provided in a container, and can be insolution at a known concentration, or can be provided in dry form, e.g.,lyophilized or freeze dried. The kit can also include buffers for use indissolving the control sample, if it is provided in dry form.

EXAMPLES A) Example 1

An OAC is a QMAX device having two plates.

The first plate is a rectangle shaped PMMA plate with a flat surface anda thickness in the range of 0.8 mm to 1.1 mm, 0.5 mm to 1.5 mm, or 0.3mm to 2 mm; a length in the range of 28 mm to 32 mm, 25 mm to 35 mm, or20 mm to 50 mm; and a width in the range of 20 mm to 28 mm, 15 mm to 34mm, or 10 mm to 40 mm.

The second plate is a rectangle shaped PMMA film with a flat surface andan array of micro pillar array imprinted on the flat surface. The PMMAfilm has a thickness in the range of 0.8 mm to 1.1 mm, 0.5 mm to 1.5 mm,or 0.3 mm to 2 mm; a length in the range of 28 mm to 32 mm, 25 mm to 35mm, or 20 mm to 50 mm; and a width in the range of 20 mm to 28 mm, 15 mmto 34 mm, or 10 mm to 40 mm. In some embodiments, when putting the firstplate and the second plate together to hold sample, at least three sidesof the second plate is inside the area of the first plate. The pillararray has a shape of either rectangle or square, a flat top, and apillar lateral size in the range of 30 um to 40 um, 25 um to 45 um, 20,um to 50 um, um to 60 um, or 5 um to 70 um, a pillar height in the rangeof 10 um to 30 um, 5 um to 40 um, 1 um to 50 um, or 0.1 um to 100 um,and a distance between two neighboring pillar center in a range of 80 to110 um, 60 to 130 um, or 30 to 180 um, or 30 to 200 um.

B) Hemoglobin Measurements Using OAC—Using One Wavelength

In an experiment of the present invention, an OAC is a QMAX device hastwo plates. The first plate is 1 mm thick flat PMMA substrate with asize of 30 mm×24 mm. The second plate is 175 um thick PMMA film with amicro pillar array on it with a size of 24 mm×22 mm. The pillar arrayhas pillar size of 30 um×40 um, pillar to pillar edge distance of 80 um,and pillar height of 10 um or 30 um.

The sample is a fresh whole blood (2.5 uL for 10 um pillar height, 5 uLfor 30 um pillar height), which was dropped in a location of the firstplate, and pressed by the second plate.

In the optical measurements, as shown in FIG. 5 , LED light are filteredby a band pass filter (532 nm to 576 nm) and illuminates onto two 45degree mirror sets. The light then goes through a semi-opaque diffuser,to eliminate coherence of the point source's wavefront and ensure theintensity change is only due to the absorption. Finally, the lighttransmits the QMAX device and is collected by a lens and camera.

The LED light and camera used here can be both from a phone.

The picture taken by camera shows that there are 2 regions. One regionis the pillar region, the other is the blood region.

The absorption of light in pillar region is neglectable. Also, theextinction coefficient of oxygenated hemoglobin [HbO2] and deoxygenatedhemoglobin [Hb] in wavelength range of 532 nm to 576 nm is similarε_(Hb)≈ε_(HbO) ₂ =44000-48000 cm⁻¹/M.

Thus, OD^(green)=ln (I/Io)=ε_(HbO) ₂ ^(greem){[Hb]+[HbO₂]}L

As shown in FIG. 6 , I is the average intensity in the blood region, Iois the average intensity in the center of the pillar region. Whencalculating the average intensity, we subtract 5 um area near the pillarboundary to reduce the analyze error.

${{Total}\mspace{14mu}{hemoglobin}\mspace{14mu}{concentration}} = {{\left\lbrack {HbO}_{2} \right\rbrack + \lbrack{Hb}\rbrack} = \frac{\ln\left( \frac{I}{Io} \right)}{ɛ \times {gap}}}$

We measured the hemoglobin in blood ranging from 6 g/dL to 11 g/dL withboth QMAX device setup and commercial Abbott Emerald hemocytometermachine and compared the results as shown in FIG. 7 . For eachconcentration, we measured 3 cards to calculate the standard deviation.

From the results, the repeatability (CV) of hemoglobin measurements byQMAX card for same blood is around 5% and the R2 value compared withgold standard is 96%.

C) Example-3

FIG. 8 . illustrates an example of a hemoglobin measurement, where theimage of an optical transmission image through a thin layer of wholeblood (without lysing) in an OAC (e.g. the sample holder described inFIG. 1 ), and the light source is a diffusive light source (e.g. a lightdiffusion is placed in front of a point light source), and the imagetaken by an iPhone. In FIG. 8 , the light-guiding spacers areperiodically placed on a QMAX card, with a vertical periodic distance of120 um and a horizontal periodic distance of 110 um.

FIG. 9 illustrates an example of the sample regions and referenceregions selected for determining hemoglobin using the image from FIG. 8. The boundary of the sampling regions and the reference are marked.

In FIG. 9 , the reference regions (with outer boundaries colored inblue) are inside light-guiding spacers; D, the distance between theedges of the reference region and the light-guiding spacer, is 10 um; d,the distance between the edges of the sampling region and thelight-guiding spacer, is 30 um; and T, the distance between the edges ofthe sampling region and the reference region, is 40 um.

D) Image Processing

According to the present invention, the image processing algorithm onhemoglobin absorption measurement consists of the following steps:

-   -   1. Light-guiding spacer detection    -   2. Reference region and sampling region determination    -   3. Individual region calculation    -   4. Polling

The light-guiding spacer detection is to detect and locate light-guidingspacers, which are periodically placed on a QMAX card. Various objectdetection algorithm can be employed, including, but not limited to,template matching, blob detection, contour detection, etc. The detectioncan be performance in a single color channel in a color space (RGB, HSV,HSI, Lab, YCrCb, etc.), such as the green channel in a RGB color space,or the hue channel in the HSV space, or a combination of two or morecolor channels, such as using red-green-blue channels in a RGB colorspace, etc.

After the periodic light-guiding spaces are detected and located, thereference regions (which are inside the light-guiding spacers) andsampling regions are selected. The sizes of reference regions andsampling regions, and the distance among the edges of the light-guidingspaces, reference regions, and sampling regions are disclosed in theinvention.

For reference regions and sampling regions, they can be associated bythe relative location and distance. When one (or more) reference regionis associated with one (or more) sampling region, a hemoglobinabsorption measurement can be calculated by the method disclosed in theinvention. One embodiment is to associate one reference region with thesampling region with the shortest distance, and calculate the hemoglobinabsorption measurement for each association.

A pooling algorithm is to pool hemoglobin absorption measurements fromeach associate and produce a single hemoglobin absorption measurement.Various pooling algorithm can be utilized, such as median, mean, max,min, k-means, etc.

In some embodiments, the imaging processing uses artificial intelligenceand/or machine learning. In some embodiments, the imaging processinguses deep learning.

E) Using Two Wavelengths

Similar to above experimental setup, except using 2 different band passfilters and taking 2 pictures.

After taking the picture, by calculating the

${OD} = {\ln\left( \frac{I}{Io} \right)}$of blood with two different wavelength λ₁ and λ₂, e.g, 660 nm and 940nm:

OD^(λ₁) = {ɛ_(Hb)^(λ₁)[Hb] + ɛ_(HbO₂)^(λ₁)[HbO₂]}LOD^(λ₂) = {ɛ_(Hb)^(λ₂)[Hb] + ɛ_(HbO₂)^(λ₂)[HbO₂]}L${{We}\mspace{14mu}{get}{\text{:}\left\lbrack {HbO}_{2} \right\rbrack}} = {{\frac{{ɛ_{Hb}^{\lambda_{2}}{OD}^{\lambda_{1}}} - {ɛ_{Hb}^{\lambda_{1}}{OD}^{\lambda_{2}}}}{L\left( {{ɛ_{Hb}^{\lambda_{2}}ɛ_{{HbO}_{2}}^{\lambda_{1}}} - {ɛ_{Hb}^{\lambda_{1}}ɛ_{{HbO}_{2}}^{\lambda_{2}}}} \right)}\lbrack{Hb}\rbrack} = \frac{{ɛ_{{HbO}_{2}}^{\lambda_{2}}{OD}^{\lambda_{1}}} - {ɛ_{{HbO}_{2}}^{\lambda_{1}}{OD}^{\lambda_{2}}}}{L\left( {{ɛ_{Hb}^{\lambda_{1}}ɛ_{{HbO}_{2}}^{\lambda_{2}}} - {ɛ_{Hb}^{\lambda_{2}}ɛ_{{HbO}_{2}}^{\lambda_{1}}}} \right)}}$

ε is the extinction coefficient of hemoglobin, [Hb] and [HbO₂] is theconcentration of hemoglobin, and L is the length of light path throughthe sample or the gap size of QMAX device.

Thus, total hemoglobin concentration=[HbO₂]+[Hb].

This method could further provide the detailed information of the ratiobetween [HbO2] and [Hb].

F) Light Guiding Spacer, Sampling Region, and Reference Region

In some embodiments, the sampling region boundary has a size of 120 umby 110 um; the edge of sampling area has a size of 60 um by 45 um; thelight guiding spacer or pillar has a size of 40 um by 30 um; thereference region has a size of 20 um by 15 um. In some embodiments, thearea of reference region is ½ of the size of the light guiding spacerarea, the distance between edge of the sampling area and that of thelight guiding spacer is ½ of the light guiding spacer area, and the areaof the sampling area is equal to the periodic inter spacer distance.

Other Descriptions and Additional Examples of Present Inventions

The present invention comprises further a combination of the disclosuresabove together a variety of embodiments that are given in the below,which can be combined in multiple ways as long as the various componentsdo not contradict one another. The embodiments should be regarded as asingle invention file: each filing has other filing as the referencesand is referenced in its entirety and for all purpose, rather than as adiscrete independent. These embodiments include not only the disclosuresin the current file, but the documents that are herein referenced,incorporated, or to which priority is claimed.

(1) Definitions

The terms used in describing the devices/apparatus, systems, and methodsherein disclosed are defined in the current application, or in PCTApplication (designating U.S.) Nos. PCT/US2016/045437 andPCT/US0216/051775, which were respectively filed on Aug. 10, 2016 andSep. 14, 2016, U.S. Provisional Application No. 62/456,065, which wasfiled on Feb. 7, 2017, US Provisional Application No. 62/456,287, whichwas filed on Feb. 8, 2017, and U.S. Provisional Application No.62/456,504, which was filed on Feb. 8, 2017, all of which applicationsare incorporated herein in their entireties for all purposes.

(2) Sample

The devices/apparatus, systems, and methods herein disclosed can beapplied to manipulation and detection of various types of samples. Thesamples are herein disclosed, listed, described, and/or summarized inPCT Application (designating U.S.) Nos. PCT/US2016/045437 andPCT/US0216/051775, which were respectively filed on Aug. 10, 2016 andSep. 14, 2016, U.S. Provisional Application No. 62/456,065, which wasfiled on Feb. 7, 2017, U.S. Provisional Application No. 62/456,287,which was filed on Feb. 8, 2017, and U.S. Provisional Application No.62/456,504, which was filed on Feb. 8, 2017, all of which applicationsare incorporated herein in their entireties for all purposes.

The devices, apparatus, systems, and methods herein disclosed can beused for samples such as but not limited to diagnostic samples, clinicalsamples, environmental samples and foodstuff samples. The types ofsample include but are not limited to the samples listed, describedand/or summarized in PCT Application (designating U.S.) Nos.PCT/US2016/045437 and PCT/US0216/051775, which were respectively filedon Aug. 10, 2016 and Sep. 14, 2016, and are hereby incorporated byreference by their entireties.

For example, in some embodiments, the devices, apparatus, systems, andmethods herein disclosed are used for a sample that comprises cells,tissues, bodily fluids and/or a mixture thereof. In some embodiments,the sample comprises a human body fluid. In some embodiments, the samplecomprises at least one of cells, tissues, bodily fluids, stool, amnioticfluid, aqueous humour, vitreous humour, blood, whole blood, fractionatedblood, plasma, serum, breast milk, cerebrospinal fluid, cerumen, chyle,chime, endolymph, perilymph, feces, gastric acid, gastric juice, lymph,mucus, nasal drainage, phlegm, pericardial fluid, peritoneal fluid,pleural fluid, pus, rheum, saliva, sebum, semen, sputum, sweat, synovialfluid, tears, vomit, urine, and exhaled breath condensate.

In some embodiments, the devices, apparatus, systems, and methods hereindisclosed are used for an environmental sample that is obtained from anysuitable source, such as but not limited to: river, lake, pond, ocean,glaciers, icebergs, rain, snow, sewage, reservoirs, tap water, drinkingwater, etc.; solid samples from soil, compost, sand, rocks, concrete,wood, brick, sewage, etc.; and gaseous samples from the air, underwaterheat vents, industrial exhaust, vehicular exhaust, etc. In certainembodiments, the environmental sample is fresh from the source; incertain embodiments, the environmental sample is processed. For example,samples that are not in liquid form are converted to liquid form beforethe subject devices, apparatus, systems, and methods are applied.

In some embodiments, the devices, apparatus, systems, and methods hereindisclosed are used for a foodstuff sample, which is suitable or has thepotential to become suitable for animal consumption, e.g., humanconsumption. In some embodiments, a foodstuff sample comprises rawingredients, cooked or processed food, plant and animal sources of food,preprocessed food as well as partially or fully processed food, etc. Incertain embodiments, samples that are not in liquid form are convertedto liquid form before the subject devices, apparatus, systems, andmethods are applied.

The subject devices, apparatus, systems, and methods can be used toanalyze any volume of the sample. Examples of the volumes include, butare not limited to, about 10 mL or less, 5 mL or less, 3 mL or less, 1microliter (pL, “uL” herein) or less, 500 μL or less, 300 μL or less,250 μL or less, 200 μL or less, 170 μL or less, 150 μL or less, 125 μLor less, 100 μL or less, 75 μL or less, 50 μL or less, pL or less, 20 μLor less, 15 μL or less, 10 μL or less, 5 μL or less, 3 μL or less, 1 μLor less, 0.5 μL or less, 0.1 μL or less, 0.05 μL or less, 0.001 μL orless, 0.0005 μL or less, 0.0001 μL or less, 10 μL or less, 1 μL or less,or a range between any two of the values.

In some embodiments, the volume of the sample includes, but is notlimited to, about 100 μL or less, 75 μL or less, 50 μL or less, 25 μL orless, 20 μL or less, 15 μL or less, 10 μL or less, 5 μL or less, 3 μL orless, 1 μL or less, 0.5 μL or less, 0.1 μL or less, 0.05 μL or less,0.001 μL or less, 0.0005 μL or less, 0.0001 μL or less, 10 μL or less, 1μL or less, or a range between any two of the values. In someembodiments, the volume of the sample includes, but is not limited to,about 10 μL or less, 5 μL or less, 3 μL or less, 1 μL or less, 0.5 μL orless, 0.1 μL or less, 0.05 μL or less, 0.001 μL or less, 0.0005 μL orless, 0.0001 μL or less, 10 μL or less, 1 μL or less, or a range betweenany two of the values.

In some embodiments, the amount of the sample is about a drop of liquid.In certain embodiments, the amount of sample is the amount collectedfrom a pricked finger or fingerstick. In certain embodiments, the amountof sample is the amount collected from a microneedle, micropipette or avenous draw.

In certain embodiments, the sample holder is configured to hold afluidic sample. In certain embodiments, the sample holder is configuredto compress at least part of the fluidic sample into a thin layer. Incertain embodiments, the sample holder comprises structures that areconfigured to heat and/or cool the sample. In certain embodiments, theheating source provides electromagnetic waves that can be absorbed bycertain structures in the sample holder to change the temperature of thesample. In certain embodiments, the signal sensor is configured todetect and/or measure a signal from the sample. In certain embodiments,the signal sensor is configured to detect and/or measure an analyte inthe sample. In certain embodiments, the heat sink is configured toabsorb heat from the sample holder and/or the heating source. In certainembodiments, the heat sink comprises a chamber that at least partlyenclose the sample holder.

(3) Q-Card, Spacers and Uniform Sample Thickness

The devices/apparatus, systems, and methods herein disclosed can includeor use Q-cards, spacers, and uniform sample thickness embodiments forsample detection, analysis, and quantification. In some embodiments, theQ-card comprises spacers, which help to render at least part of thesample into a layer of high uniformity. The structure, material,function, variation and dimension of the spacers, as well as theuniformity of the spacers and the sample layer, are herein disclosed,listed, described, and/or summarized in PCT Application (designatingU.S.) Nos. PCT/US2016/045437 and PCT/US0216/051775, which wererespectively filed on Aug. 10, 2016 and Sep. 14, 2016, U.S. ProvisionalApplication No. 62/456,065, which was filed on Feb. 7, 2017, U.S.Provisional Application No. 62/456,287, which was filed on Feb. 8, 2017,and U.S. Provisional Application No. 62/456,504, which was filed on Feb.8, 2017, all of which applications are incorporated herein in theirentireties for all purposes.

In using QMAX card, the two plates need to be open first for sampledeposition. However, in some embodiments, the QMAX card from a packagehas the two plates are in contact each other (e.g. a close position),and to separate them is challenges, since one or both plates are verything. To facilitate an opening of the QMAX card, opening notch ornotches are created at the edges or corners of the first plate or bothplaces, and, at the close position of the plates, a part of the secondplate placed over the opening notch, hence in the notch of the firstplate, the second plate can be lifted open without a blocking of thefirst plate.

In the QMAX assay platform, a QMAX card uses two plates to manipulatethe shape of a sample into a thin layer (e.g. by compressing). Incertain embodiments, the plate manipulation needs to change the relativeposition (termed: plate configuration) of the two plates several timesby human hands or other external forces. There is a need to design theQMAX card to make the hand operation easy and fast.

In QMAX assays, one of the plate configurations is an openconfiguration, wherein the two plates are completely or partiallyseparated (the spacing between the plates is not controlled by spacers)and a sample can be deposited. Another configuration is a closedconfiguration, wherein at least part of the sample deposited in the openconfiguration is compressed by the two plates into a layer of highlyuniform thickness, the uniform thickness of the layer is confined by theinner surfaces of the plates and is regulated by the plates and thespacers. In some embodiments, the average spacing between the two platesis more than 300 um.

In a QMAX assay operation, an operator needs to first make the twoplates to be in an open configuration ready for sample deposition, thendeposit a sample on one or both of the plates, and finally close theplates into a close position. In certain embodiments, the two plates ofa QMAX card are initially on top of each other and need to be separatedto get into an open configuration for sample deposition. When one of theplate is a thin plastic film (175 um thick PMA), such separation can bedifficult to perform by hand. The present invention intends to providethe devices and methods that make the operation of certain assays, suchas the QMAX card assay, easy and fast.

In some embodiments, the QMAX device comprises a hinge that connect twoor more plates together, so that the plates can open and close in asimilar fashion as a book. In some embodiments, the material of thehinge is such that the hinge can self-maintain the angle between theplates after adjustment. In some embodiments, the hinge is configured tomaintain the QMAX card in the closed configuration, such that the entireQMAX card can be slide in and slide out a card slot without causingaccidental separation of the two plates. In some embodiments, the QMAXdevice comprises one or more hinges that can control the rotation ofmore than two plates.

In some embodiments, the hinge is made from a metallic material that isselected from a group consisting of gold, silver, copper, aluminum,iron, tin, platinum, nickel, cobalt, alloys, or any combination ofthereof. In some embodiments, the hinge comprises a single layer, whichis made from a polymer material, such as but not limited to plastics.The polymer material is selected from the group consisting of acrylatepolymers, vinyl polymers, olefin polymers, cellulosic polymers,noncellulosic polymers, polyester polymers, Nylon, cyclic olefincopolymer (COC), poly(methyl methacrylate) (PMMB), polycarbonate (PC),cyclic olefin polymer (COP), liquid crystalline polymer (LCP), polyimide(PB), polyethylene (PE), polyimide (PI), polypropylene (PP),poly(phenylene ether) (PPE), polystyrene (PS), polyoxymethylene (POM),polyether ether ketone (PEEK), polyether sulfone (PES), poly(ethylenephthalate) (PET), polytetrafluoroethylene (PTFE), polyvinyl chloride(PVC), polyvinylidene fluoride (PVDF), polybutylene terephthalate (PBT),fluorinated ethylene propylene (FEP), perfluoroalkoxyalkane (PFB),polydimethylsiloxane (PDMS), rubbers, or any combinations of thereof. Insome embodiments, the polymer material is selected from polystyrene,PMMB, PC, COC, COP, other plastic, or any combination of thereof.

In essence, the term “spacers” or “stoppers” can refer to, unless statedotherwise, the mechanical objects that set, when being placed betweentwo plates, a limit on the minimum spacing between the two plates thatcan be reached when compressing the two plates together. Namely, in thecompressing, the spacers will stop the relative movement of the twoplates to prevent the plate spacing becoming less than a preset (i.e.predetermined) value.

In some embodiments, human hands can be used to press the plates into aclosed configuration; In some embodiments, human hands can be used topress the sample into a thin layer. The manners in which hand pressingis employed are described and/or summarized in PCT Application(designating U.S.) Nos. PCT/US2016/045437 filed on Aug. 10, 2016 andPCT/US0216/051775 filed on Sep. 14, 2016, and in US ProvisionalApplication Nos. 62/431,639 filed on Dec. 9, 2016, 62/456,287 filed onFeb. 8, 2017, 62/456,065 filed on Feb. 7, 2017, 62/456,504 filed on Feb.8, 2017, and 62/460,062 filed on Feb. 16, 2017, which are all herebyincorporated by reference by their entireties.

In some embodiments, human hand can be used to manipulate or handle theplates of the QMAX device. In certain embodiments, the human hand can beused to apply an imprecise force to compress the plates from an openconfiguration to a closed configuration. In certain embodiments, thehuman hand can be used to apply an imprecise force to achieve high levelof uniformity in the thickness of the sample (e.g. less than 5%, 10%,15%, or 20% variability).

(4) Hinges, Opening Notches, Recessed Edge and Sliders

The devices/apparatus, systems, and methods herein disclosed can includeor use Q-cards for sample detection, analysis, and quantification. Insome embodiments, the Q-card comprises hinges, notches, recesses, andsliders, which help to facilitate the manipulation of the Q card and themeasurement of the samples. The structure, material, function, variationand dimension of the hinges, notches, recesses, and sliders are hereindisclosed, listed, described, and/or summarized in PCT Application(designating U.S.) Nos. PCT/US2016/045437 and PCT/US0216/051775, whichwere respectively filed on Aug. 10, 2016 and Sep. 14, 2016, U.S.Provisional Application No. 62/431,639, which was filed on Dec. 9, 2016,U.S. Provisional Application No. 62/456,065, which was filed on Feb. 7,2017, U.S. Provisional Application Nos. 62/456,287 and 62/456,504, whichwas filed on Feb. 8, 2017, and U.S. Provisional Application No.62/539,660, which was filed on Aug. 1, 2017, all of which applicationsare incorporated herein in their entireties for all purposes.

In some embodiments, the QMAX device comprises opening mechanisms suchas but not limited to notches on plate edges or strips attached to theplates, making is easier for a user to manipulate the positioning of theplates, such as but not limited to separating the plates of by hand.

In some embodiments, the QMAX device comprises trenches on one or bothof the plates. In certain embodiments, the trenches limit the flow ofthe sample on the plate.

(5) Q-Card and Adaptor

The devices/apparatus, systems, and methods herein disclosed can includeor use Q-cards for sample detection, analysis, and quantification. Insome embodiments, the Q-card is used together with an adaptor that isconfigured to accommodate the Q-card and connect to a mobile device sothat the sample in the Q-card can be imaged, analyzed, and/or measuredby the mobile device. The structure, material, function, variation,dimension and connection of the Q-card, the adaptor, and the mobile areherein disclosed, listed, described, and/or summarized in PCTApplication (designating U.S.) Nos. PCT/US2016/045437 andPCT/US0216/051775, which were respectively filed on Aug. 10, 2016 andSep. 14, 2016, U.S. Provisional Application No. 62/456,065, which wasfiled on Feb. 7, 2017, US Provisional Application Nos. 62/456,287 and62/456,590, which were filed on Feb. 8, 2017, U.S. ProvisionalApplication No. 62/456,504, which was filed on Feb. 8, 2017, U.S.Provisional Application No. 62/459,544, which was filed on Feb. 15,2017, and U.S. Provisional Application Nos. 62/460,075 and 62/459,920,which were filed on Feb. 16, 2017, all of which applications areincorporated herein in their entireties for all purposes.

In some embodiments, the adaptor comprises a receptacle slot, which isconfigured to accommodate the QMAX device when the device is in a closedconfiguration. In certain embodiments, the QMAX device has a sampledeposited therein and the adaptor can be connected to a mobile device(e.g. a smartphone) so that the sample can be read by the mobile device.In certain embodiments, the mobile device can detect and/or analyze asignal from the sample. In certain embodiments, the mobile device cancapture images of the sample when the sample is in the QMAX device andpositioned in the field of view (FOV) of a camera, which in certainembodiments, is part of the mobile device.

In some embodiments, the adaptor comprises optical components, which areconfigured to enhance, magnify, and/or optimize the production of thesignal from the sample. In some embodiments, the optical componentsinclude parts that are configured to enhance, magnify, and/or optimizeillumination provided to the sample. In certain embodiments, theillumination is provided by a light source that is part of the mobiledevice. In some embodiments, the optical components include parts thatare configured to enhance, magnify, and/or optimize a signal from thesample.

(6) Smartphone Detection System

The devices/apparatus, systems, and methods herein disclosed can includeor use Q-cards for sample detection, analysis, and quantification. Insome embodiments, the Q-card is used together with an adaptor that canconnect the Q-card with a smartphone detection system. In someembodiments, the smartphone comprises a camera and/or an illuminationsource The smartphone detection system, as well the associated hardwareand software are herein disclosed, listed, described, and/or summarizedin PCT Application (designating U.S.) Nos. PCT/US2016/045437 andPCT/US0216/051775, which were respectively filed on Aug. 10, 2016 andSep. 14, 2016, U.S. Provisional Application No. 62/456,065, which wasfiled on Feb. 7, 2017, U.S. Provisional Application Nos. 62/456,287 and62/456,590, which were filed on Feb. 8, 2017, U.S. ProvisionalApplication No. 62/456,504, which was filed on Feb. 8, 2017, U.S.Provisional Application No. 62/459,544, which was filed on Feb. 15,2017, and U.S. Provisional Application Nos. 62/460,075 and 62/459,920,which were filed on Feb. 16, 2017, all of which applications areincorporated herein in their entireties for all purposes.

In some embodiments, the smartphone comprises a camera, which can beused to capture images or the sample when the sample is positioned inthe field of view of the camera (e.g. by an adaptor). In certainembodiments, the camera includes one set of lenses (e.g. as in iPhone™6). In certain embodiments, the camera includes at least two sets oflenses (e.g. as in iPhone™ 7). In some embodiments, the smartphonecomprises a camera, but the camera is not used for image capturing.

In some embodiments, the smartphone comprises a light source such as butnot limited to LED (light emitting diode). In certain embodiments, thelight source is used to provide illumination to the sample when thesample is positioned in the field of view of the camera (e.g. by anadaptor). In some embodiments, the light from the light source isenhanced, magnified, altered, and/or optimized by optical components ofthe adaptor.

In some embodiments, the smartphone comprises a processor that isconfigured to process the information from the sample. The smartphoneincludes software instructions that, when executed by the processor, canenhance, magnify, and/or optimize the signals (e.g. images) from thesample. The processor can include one or more hardware components, suchas a central processing unit (CPU), an application-specific integratedcircuit (ASIC), an application-specific instruction-set processor(ASIP), a graphics processing unit (GPU), a physics processing unit(PPU), a digital signal processor (DSP), a field-programmable gate array(FPGA), a programmable logic device (PLD), a controller, amicrocontroller unit, a reduced instruction-set computer (RISC), amicroprocessor, or the like, or any combination thereof.

In some embodiments, the smartphone comprises a communication unit,which is configured and/or used to transmit data and/or images relatedto the sample to another device. Merely by way of example, thecommunication unit can use a cable network, a wireline network, anoptical fiber network, a telecommunications network, an intranet, theInternet, a local area network (LAN), a wide area network (WAN), awireless local area network (WLAN), a metropolitan area network (MAN), awide area network (WAN), a public telephone switched network (PSTN), aBluetooth network, a ZigBee network, a near field communication (NFC)network, or the like, or any combination thereof.

In some embodiments, the smartphone is an iPhone™, an Android™ phone, ora Windows™ phone.

(7) Detection Methods

The devices/apparatus, systems, and methods herein disclosed can includeor be used in various types of detection methods. The detection methodsare herein disclosed, listed, described, and/or summarized in PCTApplication (designating U.S.) Nos. PCT/US2016/045437 andPCT/US0216/051775, which were respectively filed on Aug. 10, 2016 andSep. 14, 2016, U.S. Provisional Application No. 62/456,065, which wasfiled on Feb. 7, 2017, U.S. Provisional Application Nos. 62/456,287,62/456,528, 62/456,631, 62/456,522, 62/456,598, 62/456,603, and62/456,628, which were filed on Feb. 8, 2017, U.S. ProvisionalApplication Nos. 62/459,276, 62/456,904, 62/457,075, and 62/457,009,which were filed on Feb. 9, 2017, and U.S. Provisional Application Nos.62/459,303, 62/459,337, and 62/459,598, which were filed on Feb. 15,2017, and U.S. Provisional Application No. 62/460,083, 62/460,076, whichwere filed on Feb. 16, 2017, all of which applications are incorporatedherein in their entireties for all purposes.

(8) Labels, Capture Agent and Detection Agent

The devices/apparatus, systems, and methods herein disclosed can employvarious types of labels, capture agents, and detection agents that areused for analytes detection. The labels are herein disclosed, listed,described, and/or summarized in PCT Application (designating U.S.) Nos.PCT/US2016/045437 and PCT/US0216/051775, which were respectively filedon Aug. 10, 2016 and Sep. 14, 2016, U.S. Provisional Application No.62/456,065, which was filed on Feb. 7, 2017, U.S. ProvisionalApplication No. 62/456,287, which was filed on Feb. 8, 2017, and U.S.Provisional Application No. 62/456,504, which was filed on Feb. 8, 2017,all of which applications are incorporated herein in their entiretiesfor all purposes.

In some embodiments, the label is optically detectable, such as but notlimited to a fluorescence label. In some embodiments, the labelsinclude, but are not limited to, IRDye800CW, Alexa 790, Dylight 800,fluorescein, fluorescein isothiocyanate, succinimidyl esters ofcarboxyfluorescein, succinimidyl esters of fluorescein, 5-isomer offluorescein dichlorotriazine, cagedcarboxyfluorescein-alanine-carboxamide, Oregon Green 488, Oregon Green514; Lucifer Yellow, acridine Orange, rhodamine, tetramethylrhodamine,Texas Red, propidium iodide, JC-1(5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethylbenzimidazoylcarbocyanineiodide), tetrabromorhodamine 123, rhodamine 6G, TMRM (tetramethylrhodamine methyl ester), TMRE (tetramethyl rhodamine ethyl ester),tetramethylrosamine, rhodamine B and 4-dimethylaminotetramethylrosamine,green fluorescent protein, blue-shifted green fluorescent protein,cyan-shifted green fluorescent protein, red-shifted green fluorescentprotein, yellow-shifted green fluorescent protein,4-acetamido-4′-isothiocyanatostilbene-2,2′disulfonic acid; acridine andderivatives, such as acridine, acridine isothiocyanate;5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS);4-amino-N-[3-vinylsulfonyl)phenyl]naphth-alimide-3,5 disulfonate;N-(4-anilino-1-naphthyl)maleimide; anthranilamide;4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a diaza-5-indacene-3-propioni-cacid BODIPY; cascade blue; Brilliant Yellow; coumarin and derivatives:coumarin, 7-amino-4-methylcoumarin (AMC, Coumarin 120),7-amino-4-trifluoromethylcoumarin (Coumarin 151); cyanine dyes;cyanosine; 4′,6-diaminidino-2-phenylindole (DAPI);5′,5″-dibromopyrogallol-sulfonaphthalein (Bromopyrogallol Red);7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin;diethylenetriaamine pentaacetate;4,4′-diisothiocyanatodihydro-stilbene-2-, 2′-disulfonic acid;4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid;5-(dimethylamino]naphthalene-1-sulfonyl chloride (DNS, dansylchloride);4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC); eosin andderivatives: eosin, eosin isothiocyanate, erythrosin and derivatives:erythrosin B, erythrosin, isothiocyanate; ethidium; fluorescein andderivatives: 5-carboxyfluorescein (FAM),5-(4,6-dichlorotriazin-2-yl)amino-fluorescein (DTAF),2′,7′dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), fluorescein,fluorescein isothiocyanate, QFITC, (XRITC); fluorescamine; IR144;IR1446; Malachite Green isothiocyanate; 4-methylumbelli-feroneorthocresolphthalein; nitrotyrosine; pararosaniline; Phenol Red;B-phycoerythrin; o-phthaldialdehyde; pyrene and derivatives: pyrene,pyrene butyrate, succinimidyl 1-pyrene; butyrate quantum dots; ReactiveRed 4 (Cibacron™ Brilliant Red 3B-A) rhodamine and derivatives:6-carboxy-X-rhodamine (ROX), 6-carboxyrhodamine (R6G), lissaminerhodamine B sulfonyl chloride rhodamine (Rhod), rhodamine B, rhodamine123, rhodamine X isothiocyanate, sulforhodamine B, sulforhodamine 101,sulfonyl chloride derivative of sulforhodamine 101 (Texas Red);N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA); tetramethyl rhodamine;tetramethyl hodamine isothiocyanate (TRITC); riboflavin;5-(2′-aminoethyl) am inonaphthalene-1-sulfonic acid (EDANS),4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL), rosolic acid; CALFluor Orange 560; terbium chelate derivatives; Cy 3; Cy 5; Cy 5.5; Cy 7;IRD 700; IRD 800; La Jolla Blue; phthalo cyanine; and naphthalo cyanine,coumarins and related dyes, xanthene dyes such as rhodols, resorufins,bimanes, acridines, isoindoles, dansyl dyes, aminophthalic hydrazidessuch as luminol, and isoluminol derivatives, aminophthalimides,aminonaphthalimides, aminobenzofurans, aminoquinolines,dicyanohydroquinones, fluorescent europium and terbium complexes;combinations thereof, and the like. Suitable fluorescent proteins andchromogenic proteins include, but are not limited to, a greenfluorescent protein (GFP), including, but not limited to, a GFP derivedfrom Aequoria victoria or a derivative thereof, e.g., a “humanized”derivative such as Enhanced GFP; a GFP from another species such asRenilla reniformis, Renilla mulleri, or Ptilosarcus guernyi; “humanized”recombinant GFP (hrGFP); any of a variety of fluorescent and coloredproteins from Anthozoan species; combinations thereof; and the like.

In any embodiment, the QMAX device can contain a plurality of captureagents and/or detection agents that each bind to a biomarker selectedfrom Tables B1, B2, B3 and/or B7 in U.S. Provisional Application No.62/234,538 and/or PCT Application No. PCT/US2016/054025, wherein thereading step d) includes obtaining a measure of the amount of theplurality of biomarkers in the sample, and wherein the amount of theplurality of biomarkers in the sample is diagnostic of a disease orcondition.

In any embodiment, the capture agent and/or detection agents can be anantibody epitope and the biomarker can be an antibody that binds to theantibody epitope. In some embodiments, the antibody epitope includes abiomolecule, or a fragment thereof, selected from Tables B4, B5 or B6 inU.S. Provisional Application No. 62/234,538 and/or PCT Application No.PCT/US2016/054025. In some embodiments, the antibody epitope includes anallergen, or a fragment thereof, selected from Table B5. In someembodiments, the antibody epitope includes an infectious agent-derivedbiomolecule, or a fragment thereof, selected from Table B6 in U.S.Provisional Application No. 62/234,538 and/or PCT Application No.PCT/US2016/054025.

In any embodiment, the QMAX device can contain a plurality of antibodyepitopes selected from Tables B4, B5 and/or B6 in U.S. ProvisionalApplication No. 62/234,538 and/or PCT Application No. PCT/US2016/054025,wherein the reading step d) includes obtaining a measure of the amountof a plurality of epitope-binding antibodies in the sample, and whereinthe amount of the plurality of epitope-binding antibodies in the sampleis diagnostic of a disease or condition.

(9) Analytes

The devices/apparatus, systems, and methods herein disclosed can beapplied to manipulation and detection of various types of analytes(including biomarkers). The analytes are herein disclosed, listed,described, and/or summarized in PCT Application (designating U.S.) Nos.PCT/US2016/045437 and PCT/US0216/051775, which were respectively filedon Aug. 10, 2016 and Sep. 14, 2016, U.S. Provisional Application No.62/456,065, which was filed on Feb. 7, 2017, U.S. ProvisionalApplication No. 62/456,287, which was filed on Feb. 8, 2017, and U.S.Provisional Application No. 62/456,504, which was filed on Feb. 8, 2017,all of which applications are incorporated herein in their entiretiesfor all purposes.

The devices, apparatus, systems, and methods herein disclosed can beused for the detection, purification and/or quantification of variousanalytes. In some embodiments, the analytes are biomarkers thatassociated with various diseases. In some embodiments, the analytesand/or biomarkers are indicative of the presence, severity, and/or stageof the diseases. The analytes, biomarkers, and/or diseases that can bedetected and/or measured with the devices, apparatus, systems, and/ormethod of the present invention include the analytes, biomarkers, and/ordiseases listed, described and/or summarized in PCT Application(designating U.S.) Nos. PCT/US2016/045437 filed on Aug. 10, 2016, andPCT Application No. PCT/US2016/054025 filed on Sep. 27, 2016, and U.S.Provisional Application Nos. 62/234,538 filed on Sep. 29, 2015,62/233,885 filed on Sep. 28, 2015, 62/293,188 filed on Feb. 9, 2016, and62/305,123 filed on Mar. 8, 2016, which are all hereby incorporated byreference by their entireties. For example, the devices, apparatus,systems, and methods herein disclosed can be used in (a) the detection,purification and quantification of chemical compounds or biomoleculesthat correlates with the stage of certain diseases, e.g., infectious andparasitic disease, injuries, cardiovascular disease, cancer, mentaldisorders, neuropsychiatric disorders and organic diseases, e.g.,pulmonary diseases, renal diseases, (b) the detection, purification andquantification of microorganism, e.g., virus, fungus and bacteria fromenvironment, e.g., water, soil, or biological samples, e.g., tissues,bodily fluids, (c) the detection, quantification of chemical compoundsor biological samples that pose hazard to food safety or nationalsecurity, e.g. toxic waste, anthrax, (d) quantification of vitalparameters in medical or physiological monitor, e.g., glucose, bloodoxygen level, total blood count, (e) the detection and quantification ofspecific DNA or RNA from biosamples, e.g., cells, viruses, bodilyfluids, (f) the sequencing and comparing of genetic sequences in DNA inthe chromosomes and mitochondria for genome analysis or (g) to detectreaction products, e.g., during synthesis or purification ofpharmaceuticals.

In some embodiments, the analyte can be a biomarker, an environmentalmarker, or a foodstuff marker. The sample in some instances is a liquidsample, and can be a diagnostic sample (such as saliva, serum, blood,sputum, urine, sweat, lacrima, semen, or mucus); an environmental sampleobtained from a river, ocean, lake, rain, snow, sewage, sewageprocessing runoff, agricultural runoff, industrial runoff, tap water ordrinking water; or a foodstuff sample obtained from tap water, drinkingwater, prepared food, processed food or raw food.

In any embodiment, the sample can be a diagnostic sample obtained from asubject, the analyte can be a biomarker, and the measured the amount ofthe analyte in the sample can be diagnostic of a disease or a condition.

In any embodiment, the devices, apparatus, systems, and methods in thepresent invention can further include diagnosing the subject based oninformation including the measured amount of the biomarker in thesample. In some cases, the diagnosing step includes sending datacontaining the measured amount of the biomarker to a remote location andreceiving a diagnosis based on information including the measurementfrom the remote location.

In any embodiment, the biomarker can be selected from Tables B1, 2, 3 or7 as disclosed in U.S. Provisional Application Nos. 62/234,538,62/293,188, and/or 62/305,123, and/or PCT Application No.PCT/US2016/054,025, which are all incorporated in their entireties forall purposes. In some instances, the biomarker is a protein selectedfrom Tables B1, 2, or 3. In some instances, the biomarker is a nucleicacid selected from Tables B2, 3 or 7. In some instances, the biomarkeris an infectious agent-derived biomarker selected from Table B2. In someinstances, the biomarker is a microRNA (miRNA) selected from Table B7.

In any embodiment, the applying step b) can include isolating miRNA fromthe sample to generate an isolated miRNA sample, and applying theisolated miRNA sample to the disk-coupled dots-on-pillar antenna (QMAXdevice) array.

In any embodiment, the QMAX device can contain a plurality of captureagents that each bind to a biomarker selected from Tables B1, B2, B3and/or B7, wherein the reading step d) includes obtaining a measure ofthe amount of the plurality of biomarkers in the sample, and wherein theamount of the plurality of biomarkers in the sample is diagnostic of adisease or condition.

In any embodiment, the capture agent can be an antibody epitope and thebiomarker can be an antibody that binds to the antibody epitope. In someembodiments, the antibody epitope includes a biomolecule, or a fragmentthereof, selected from Tables B4, B5 or B6. In some embodiments, theantibody epitope includes an allergen, or a fragment thereof, selectedfrom Table B5. In some embodiments, the antibody epitope includes aninfectious agent-derived biomolecule, or a fragment thereof, selectedfrom Table B6.

In any embodiment, the QMAX device can contain a plurality of antibodyepitopes selected from Tables B4, B5 and/or B6, wherein the reading stepd) includes obtaining a measure of the amount of a plurality ofepitope-binding antibodies in the sample, and wherein the amount of theplurality of epitope-binding antibodies in the sample is diagnostic of adisease or condition.

In any embodiment, the sample can be an environmental sample, andwherein the analyte can be an environmental marker. In some embodiments,the environmental marker is selected from Table B8 in U.S. ProvisionalApplication No. 62/234,538 and/or PCT Application No. PCT/US2016/054025.

In any embodiment, the method can include receiving or providing areport that indicates the safety or harmfulness for a subject to beexposed to the environment from which the sample was obtained.

In any embodiment, the method can include sending data containing themeasured amount of the environmental marker to a remote location andreceiving a report that indicates the safety or harmfulness for asubject to be exposed to the environment from which the sample wasobtained.

In any embodiment, the QMAX device array can include a plurality ofcapture agents that each binds to an environmental marker selected fromTable B8, and wherein the reading step d) can include obtaining ameasure of the amount of the plurality of environmental markers in thesample.

In any embodiment, the sample can be a foodstuff sample, wherein theanalyte can be a foodstuff marker, and wherein the amount of thefoodstuff marker in the sample can correlate with safety of thefoodstuff for consumption. In some embodiments, the foodstuff marker isselected from Table B9.

In any embodiment, the method can include receiving or providing areport that indicates the safety or harmfulness for a subject to consumethe foodstuff from which the sample is obtained.

In any embodiment, the method can include sending data containing themeasured amount of the foodstuff marker to a remote location andreceiving a report that indicates the safety or harmfulness for asubject to consume the foodstuff from which the sample is obtained.

In any embodiment, the devices, apparatus, systems, and methods hereindisclosed can include a plurality of capture agents that each binds to afoodstuff marker selected from Table B9 from in U.S. ProvisionalApplication No. 62/234,538 and PCT Application No. PCT/US2016/054025,wherein the obtaining can include obtaining a measure of the amount ofthe plurality of foodstuff markers in the sample, and wherein the amountof the plurality of foodstuff marker in the sample can correlate withsafety of the foodstuff for consumption.

provided herein are kits that find use in practicing the devices,systems and methods in the present invention.

The amount of sample can be about a drop of a sample. The amount ofsample can be the amount collected from a pricked finger or fingerstick.The amount of sample can be the amount collected from a microneedle or avenous draw.

A sample can be used without further processing after obtaining it fromthe source, or can be processed, e.g., to enrich for an analyte ofinterest, remove large particulate matter, dissolve or resuspend a solidsample, etc.

Any suitable method of applying a sample to the QMAX device can beemployed. Suitable methods can include using a pipet, dropper, syringe,etc. In certain embodiments, when the QMAX device is located on asupport in a dipstick format, as described below, the sample can beapplied to the QMAX device by dipping a sample-receiving area of thedipstick into the sample.

A sample can be collected at one time, or at a plurality of times.Samples collected over time can be aggregated and/or processed (byapplying to a QMAX device and obtaining a measurement of the amount ofanalyte in the sample, as described herein) individually. In someinstances, measurements obtained over time can be aggregated and can beuseful for longitudinal analysis over time to facilitate screening,diagnosis, treatment, and/or disease prevention.

Washing the QMAX device to remove unbound sample components can be donein any convenient manner, as described above. In certain embodiments,the surface of the QMAX device is washed using binding buffer to removeunbound sample components.

Detectable labeling of the analyte can be done by any convenient method.The analyte can be labeled directly or indirectly. In direct labeling,the analyte in the sample is labeled before the sample is applied to theQMAX device. In indirect labeling, an unlabeled analyte in a sample islabeled after the sample is applied to the QMAX device to capture theunlabeled analyte, as described below.

(10) Applications

The devices/apparatus, systems, and methods herein disclosed can be usedfor various applications (fields and samples). The applications areherein disclosed, listed, described, and/or summarized in PCTApplication (designating U.S.) Nos. PCT/US2016/045437 andPCT/US0216/051775, which were respectively filed on Aug. 10, 2016 andSep. 14, 2016, U.S. Provisional Application No. 62/456,065, which wasfiled on Feb. 7, 2017, U.S. Provisional Application No. 62/456,287,which was filed on Feb. 8, 2017, and U.S. Provisional Application No.62/456,504, which was filed on Feb. 8, 2017, all of which applicationsare incorporated herein in their entireties for all purposes.

In some embodiments, the devices, apparatus, systems, and methods hereindisclosed are used in a variety of different application in variousfield, wherein determination of the presence or absence, quantification,and/or amplification of one or more analytes in a sample are desired.For example, in certain embodiments the subject devices, apparatus,systems, and methods are used in the detection of proteins, peptides,nucleic acids, synthetic compounds, inorganic compounds, organiccompounds, bacteria, virus, cells, tissues, nanoparticles, and othermolecules, compounds, mixtures and substances thereof. The variousfields in which the subject devices, apparatus, systems, and methods canbe used include, but are not limited to: diagnostics, management, and/orprevention of human diseases and conditions, diagnostics, management,and/or prevention of veterinary diseases and conditions, diagnostics,management, and/or prevention of plant diseases and conditions,agricultural uses, veterinary uses, food testing, environments testingand decontamination, drug testing and prevention, and others.

The applications of the present invention include, but are not limitedto: (a) the detection, purification, quantification, and/oramplification of chemical compounds or biomolecules that correlates withcertain diseases, or certain stages of the diseases, e.g., infectiousand parasitic disease, injuries, cardiovascular disease, cancer, mentaldisorders, neuropsychiatric disorders and organic diseases, e.g.,pulmonary diseases, renal diseases, (b) the detection, purification,quantification, and/or amplification of cells and/or microorganism,e.g., virus, fungus and bacteria from the environment, e.g., water,soil, or biological samples, e.g., tissues, bodily fluids, (c) thedetection, quantification of chemical compounds or biological samplesthat pose hazard to food safety, human health, or national security,e.g. toxic waste, anthrax, (d) the detection and quantification of vitalparameters in medical or physiological monitor, e.g., glucose, bloodoxygen level, total blood count, (e) the detection and quantification ofspecific DNA or RNA from biological samples, e.g., cells, viruses,bodily fluids, (f) the sequencing and comparing of genetic sequences inDNA in the chromosomes and mitochondria for genome analysis or (g) thedetection and quantification of reaction products, e.g., duringsynthesis or purification of pharmaceuticals.

In some embodiments, the subject devices, apparatus, systems, andmethods are used in the detection of nucleic acids, proteins, or othermolecules or compounds in a sample. In certain embodiments, the devices,apparatus, systems, and methods are used in the rapid, clinicaldetection and/or quantification of one or more, two or more, or three ormore disease biomarkers in a biological sample, e.g., as being employedin the diagnosis, prevention, and/or management of a disease conditionin a subject. In certain embodiments, the devices, apparatus, systems,and methods are used in the detection and/or quantification of one ormore, two or more, or three or more environmental markers in anenvironmental sample, e.g. sample obtained from a river, ocean, lake,rain, snow, sewage, sewage processing runoff, agricultural runoff,industrial runoff, tap water or drinking water. In certain embodiments,the devices, apparatus, systems, and methods are used in the detectionand/or quantification of one or more, two or more, or three or morefoodstuff marks from a food sample obtained from tap water, drinkingwater, prepared food, processed food or raw food.

In some embodiments, the subject device is part of a microfluidicdevice. In some embodiments, the subject devices, apparatus, systems,and methods are used to detect a fluorescence or luminescence signal. Insome embodiments, the subject devices, apparatus, systems, and methodsinclude, or are used together with, a communication device, such as butnot limited to: mobile phones, tablet computers and laptop computers. Insome embodiments, the subject devices, apparatus, systems, and methodsinclude, or are used together with, an identifier, such as but notlimited to an optical barcode, a radio frequency ID tag, or combinationsthereof.

In some embodiments, the sample is a diagnostic sample obtained from asubject, the analyte is a biomarker, and the measured amount of theanalyte in the sample is diagnostic of a disease or a condition. In someembodiments, the subject devices, systems and methods further includereceiving or providing to the subject a report that indicates themeasured amount of the biomarker and a range of measured values for thebiomarker in an individual free of or at low risk of having the diseaseor condition, wherein the measured amount of the biomarker relative tothe range of measured values is diagnostic of a disease or condition.

In some embodiments, the sample is an environmental sample, and whereinthe analyte is an environmental marker. In some embodiments, the subjectdevices, systems and methods includes receiving or providing a reportthat indicates the safety or harmfulness for a subject to be exposed tothe environment from which the sample was obtained. In some embodiments,the subject devices, systems and methods include sending data containingthe measured amount of the environmental marker to a remote location andreceiving a report that indicates the safety or harmfulness for asubject to be exposed to the environment from which the sample wasobtained.

In some embodiments, the sample is a foodstuff sample, wherein theanalyte is a foodstuff marker, and wherein the amount of the foodstuffmarker in the sample correlate with safety of the foodstuff forconsumption. In some embodiments, the subject devices, systems andmethods include receiving or providing a report that indicates thesafety or harmfulness for a subject to consume the foodstuff from whichthe sample is obtained. In some embodiments, the subject devices,systems and methods include sending data containing the measured amountof the foodstuff marker to a remote location and receiving a report thatindicates the safety or harmfulness for a subject to consume thefoodstuff from which the sample is obtained.

(11) Dimensions

The devices, apparatus, systems, and methods herein disclosed caninclude or use a QMAX device, which can comprise plates and spacers. Insome embodiments, the dimension of the individual components of the QMAXdevice and its adaptor are listed, described and/or summarized in PCTApplication (designating U.S.) No. PCT/US2016/045437 filed on Aug. 10,2016, and U.S. Provisional Application Nos. 62,431,639 filed on Dec. 9,2016 and 62/456,287 filed on Feb. 8, 2017, which are all herebyincorporated by reference by their entireties.

In some embodiments, the dimensions are listed in the Tables below:

Plates:

Parameters Embodiments Preferred Embodiments Shape round, ellipse,rectangle, at least one of the two (or triangle, polygonal, ring-shaped,more) plates of the or any superposition of these QMAX card has roundshapes; the two (or more) plates corners for user safety of the QMAXcard can have the concerns, wherein the same size and/or shape, or roundcorners have a different size and/or shape; diameter of 100 um or less,200 um or less, 500 um or less, 1 mm or less, 2 mm or less, 5 mm orless, 10 mm or less, 50 mm or less, or in a range between any two of thevalues. Thickness the average thickness for at least For at least one ofthe one of the plates is 2 nm or less, plates is in the range of 10 nmor less, 100 nm or less, 0.5 to 1.5 mm; around 1 200 nm or less, 500 nmor less, mm; in the range of 0.15 1000 nm or less, 2 μm (micron) to 0.2mm; or around or less, 5 μm or less, 10 μm or 0.175 mm less, 20 μm orless, 50 μm or less, 100 μm or less, 150 μm or less, 200 μm or less, 300μm or less, 500 μm or less, 800 μm or less, 1 mm (millimeter) or less, 2mm or less, 3 mm or less, 5 mm or less, 10 mm or less, 20 mm or less, 50mm or less, 100 mm or less, 500 mm or less, or in a range between anytwo of these values Lateral For at least one of the plate is 1 For atleast one plate of Area mm2 (square millimeter) or less, the QMAX cardis in the 10 mm2 or less, 25 mm2 or less, range of 500 to 1000 50 mm2 orless, 75 mm2 or less, mm²; or around 750 1 cm2 (square centimeter) ormm². less, 2 cm2 or less, 3 cm2 or less, 4 cm2 or less, 5 cm2 or less,10 cm2 or less, 100 cm2 or less, 500 cm2 or less, 1000 cm2 or less, 5000cm2 or less, 10,000 cm2 or less, 10,000 cm2 or less, or in a rangebetween any two of these values Lateral For at least one of the platesof For at least one plate of Linear the QMAX card is 1 mm or less, theQMAX card is in the Dimension 5 mm or less, 10 mm or less, 15 range of20 to 30 mm; or (width, mm or less, 20 mm or less, 25 around 24 mmlength, or mm or less, 30 mm or less, 35 diameter, mm or less, 40 mm orless, 45 etc.) mm or less, 50 mm or less, 100 mm or less, 200 mm orless, 500 mm or less, 1000 mm or less, 5000 mm or less, or in a rangebetween any two of these values Recess 1 um or less, 10 um or less, 20In the range of 1 mm to width um or less, 30 um or less, 40 um 10 mm; Oror less, 50 um or less, 100 um or About 5 mm less, 200 um or less, 300um or less, 400 um or less, 500 um or less, 7500 um or less, 1 mm orless, 5 mm or less, 10 mm or less, 100 mm or less, or 1000 mm or less,or in a range between any two of these values.Hinge:

Parameters Embodiments Preferred Embodiments Number 1, 2, 3, 4, 5, ormore 1 or 2 Length of 1 mm or less, 2 mm or less, 3 In the range of 5 mmto Hinge Joint mm or less, 4 mm or less, 5 30 mm. mm or less, 10 mm orless, 15 mm or less, 20 mm or less, 25 mm or less, 30 mm or less, 40 mmor less, 50 mm or less, 100 mm or less, 200 mm or less, or 500 mm orless, or in a range between anytwo of these values Ratio (hinge 1.5 orless, 1 or less, 0.9 or In the range of 0.2 to joint length less, 0.8 orless, 0.7 or less, 1; or about 1 vs. aligning 0.6 or less, 0.5 or less,0.4 or plate edge less, 0.3 or less, 0.2 or less, length 0.1 or less,0.05 or less or in a range between any two of these values. Area 1 mm²or less, 5 mm² or less, In the range of 20 to 10 mm² or less, 20 mm² or200 mm²; or about 120 less, 30 mm² or less, 40 mm² mm² or less, 50 mm²or less, 100 mm² or less, 200 mm² or less, 500 mm² or less, or in arange between any of the two values Ratio (hinge 1 or less, 0.9 or less,0.8 or In the range of 0.05 to area vs. less, 0.7 or less, 0.6 or less,0.2, around 0.15 plate area) 0.5 or less, 0.4 or less, 0.3 or less, 0.2or less, 0.1 or less, 0.05 or less, 0.01 orless or in a range betweenany two of these values Max. Open 15 or less, 30 or less, 45 or In therange of 90 to Degree less, 60 or less, 75 or less, 90 180 degrees orless, 105 or less, 120 or less, 135 or less, 150 or less, 165 or less,180 or less, 195 or less, 210 or less, 225 or less, 240 or less, 255 orless, 270 or less, 285 or less, 300 or less, 315 or less, 330 or less,345 or less or 360 or less degrees, or in a range between any two ofthese values No. of 1, 2, 3, 4, 5, or more 1 or 2 Layers Layer 0.1 um orless, 1 um or less, 2 In the range of 20 um thickness um or less, 3 umor less, 5 um to 1 mm; or or less, 10 um or less, 20 um Around 50 um orless, 30 um or less, 50 um or less, 100 um or less, 200 um or less, 300um or less, 500 um or less, 1 mm or less, 2 mm or less, and a rangebetween any two of these values Angle- Limiting the angle adjustment Nomore than ±2 maintaining with no more than ±90, ±45, ±30, ±25, ±20, ±15,±10, ±8, ±6, ±5, ±4, ±3, ±2, or ±1, or in a range between any two ofthese valuesNotch:

Parameters Embodiments Preferred Embodiments Number 1, 2, 3, 4, 5, ormore 1 or 2 Shape round, ellipse, rectangle, Part of a circle triangle,polygon, ring-shaped, or any superposition or portion of these shapes.Positioning Any location along any edge except the hinge edge, or anycorner joint by non-hinge edges Lateral 1 mm or less, 2.5 mm or In therange of 5 mm to Linear less, 5 mm or less, 10 mm 15 mm; or about 10 mmDimension or less, 15 mm or less, 20 (Length mm or less, 25 mm or less,along the 30 mm or less, 40 mm or edge, less, 50 mm or less, or in aradius, etc.) range between any two of these values Area 1 mm² (squaremillimeter) In the range of 10 to 150 or less, 10 mm² or less, 25 mm²;or about 50 mm² mm² or less, 50 mm² or less, 75 mm² or less or in arange between any two of these values.Trench:

Preferred Parameters Embodiments Embodiments Number 1, 2, 3, 4, 5, ormore 1 or 2 Shape Closed (round, ellipse, rectangle, triangle, polygon,ring-shaped, or any superposition or portion of these shapes) oropen-ended (straight line, curved line, arc, branched tree, or any othershape with open endings); Length 0.001 mm or less, 0.005 mm or less,0.01 mm or less, 0.05 mm or less, 0.1 mm or less, 0.5 mm or less, 1 mmor less, 2 mm or less, 5 mm or less, 10 mm or less, 20 mm or less, 50 mmor less, 100 mm or less, or in a range between any two of these valuesCross- 0.001 mm² or less, 0.005 mm² or less, sectional 0.01 mm² or less,0.05 mm² or less, 0.1 Area mm² or less, 0.5 mm² or less, 1 mm² or less,2 mm² or less, 5 mm² or less, 10 mm² or less, 20 mm² or less, or in arange between any two of these values. Volume 0.1 uL or more, 0.5 uL ormore, 1 uL or In the range of 1 more, 2 uL or more, 5 uL or more, 10 uLto 20 uL; or uL or more, 30 uL or more, 50 uL or About 5 uL more, 100 uLor more, 500 uL or more, 1 mL or more, or in a range between any two ofthese valuesReceptacle Slot

Preferred Parameters Embodiments Embodiments Shape of round, ellipse,rectangle, triangle, receiving polygon, ring-shaped, or any areasuperposition of these shapes; Difference 100 nm, 500 nm, 1 um, 2 um, 5um, In the range of between 10 um, 50 um, 100 um, 300 um, 500 50 to 300um; or sliding track um, 1 mm, 2 mm, 5 mm, 1 cm, or in about 75 um gapsize a range between any two of the and card values. thicknessDifference 1 mm² (square millimeter) or less, 10 between mm² or less, 25mm² or less, 50 mm² receiving or less, 75 mm² or less, 1 cm² (squarearea and centimeter) or less, 2 cm² or less, 3 card area cm² or less, 4cm² or less, 5 cm² or less, 10 cm² or less, 100 cm² or less, or in arange between any of the two values.

(12) Cloud

The devices/apparatus, systems, and methods herein disclosed can employcloud technology for data transfer, storage, and/or analysis. Therelated cloud technologies are herein disclosed, listed, described,and/or summarized in PCT Application (designating U.S.) Nos.PCT/US2016/045437 and PCT/US0216/051775, which were respectively filedon Aug. 10, 2016 and Sep. 14, 2016, U.S. Provisional Application No.62/456,065, which was filed on Feb. 7, 2017, U.S. ProvisionalApplication No. 62/456,287, which was filed on Feb. 8, 2017, and U.S.Provisional Application No. 62/456,504, which was filed on Feb. 8, 2017,all of which applications are incorporated herein in their entiretiesfor all purposes.

In some embodiments, the cloud storage and computing technologies caninvolve a cloud database. Merely by way of example, the cloud platformcan include a private cloud, a public cloud, a hybrid cloud, a communitycloud, a distributed cloud, an inter-cloud, a multi-cloud, or the like,or any combination thereof. In some embodiments, the mobile device (e.g.smartphone) can be connected to the cloud through any type of network,including a local area network (LAN) or a wide area network (WAN).

In some embodiments, the data (e.g. images of the sample) related to thesample is sent to the cloud without processing by the mobile device andfurther analysis can be conducted remotely. In some embodiments, thedata related to the sample is processed by the mobile device and theresults are sent to the cloud. In some embodiments, both the raw dataand the results are transmitted to the cloud.

Other Embodiments

Further examples of inventive subject matter according to the presentdisclosure are described in the following enumerated paragraphs.

It must be noted that, as used herein and in the appended claims, thesingular forms “a”, “an”, and “the” include plural referents unless thecontext clearly dictates otherwise, e.g., when the word “single” isused. For example, reference to “an analyte” includes a single analyteand multiple analytes, reference to “a capture agent” includes a singlecapture agent and multiple capture agents, reference to “a detectionagent” includes a single detection agent and multiple detection agents,and reference to “an agent” includes a single agent and multiple agents.

Ranges can be expressed herein as from “about” one particular value,and/or to “about” another particular value. When such a range isexpressed, another embodiment includes from the one particular valueand/or to the other particular value. Similarly, when values areexpressed as approximations, by use of the antecedent “about,” it willbe understood that the particular value forms another embodiment. Itwill be further understood that the endpoints of each of the ranges aresignificant both in relation to the other endpoint, and independently ofthe other endpoint. The term “about” or “approximately” can mean withinan acceptable error range for the particular value as determined by oneof ordinary skill in the art, which will depend in part on how the valueis measured or determined, e.g. the limitations of the measurementsystem. For example, “about” can mean within 1 or more than 1 standarddeviation, per the practice in the art. Alternatively, “about” can meana range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value.Alternatively, particularly with respect to biological systems orprocesses, the term can mean within an order of magnitude, within5-fold, and more preferably within 2-fold, of a value. Where particularvalues are described in the application and claims, unless otherwisestated the term “about” meaning within an acceptable error range for theparticular value should be assumed. The term “about” has the meaning ascommonly understood by one of ordinary skill in the art. In certainembodiments, the term “about” can refer to ±10%. In certain embodiments,the term “about” can refer to ±5%.

As used herein, the terms “adapted” and “configured” mean that theelement, component, or other subject matter is designed and/or intendedto perform a given function. Thus, the use of the terms “adapted” and“configured” should not be construed to mean that a given element,component, or other subject matter is simply “capable of” performing agiven function. Similarly, subject matter that is recited as beingconfigured to perform a particular function can additionally oralternatively be described as being operative to perform that function.

As used herein, the phrase, “for example,” the phrase, “as an example,”and/or simply the terms “example” and “exemplary” when used withreference to one or more components, features, details, structures,embodiments, and/or methods according to the present disclosure, areintended to convey that the described component, feature, detail,structure, embodiment, and/or method is an illustrative, non-exclusiveexample of components, features, details, structures, embodiments,and/or methods according to the present disclosure. Thus, the describedcomponent, feature, detail, structure, embodiment, and/or method is notintended to be limiting, required, or exclusive/exhaustive; and othercomponents, features, details, structures, embodiments, and/or methods,including structurally and/or functionally similar and/or equivalentcomponents, features, details, structures, embodiments, and/or methods,are also within the scope of the present disclosure.

As used herein, the phrases “at least one of” and “one or more of,” inreference to a list of more than one entity, means any one or more ofthe entity in the list of entity, and is not limited to at least one ofeach and every entity specifically listed within the list of entity. Forexample, “at least one of A and B” (or, equivalently, “at least one of Aor B,” or, equivalently, “at least one of A and/or B”) can refer to Aalone, B alone, or the combination of A and B.

As used herein, the term “and/or” placed between a first entity and asecond entity means one of (1) the first entity, (2) the second entity,and (3) the first entity and the second entity. Multiple entity listedwith “and/or” should be construed in the same manner, e.g., “one ormore” of the entity so conjoined. Other entity can optionally be presentother than the entity specifically identified by the “and/or” clause,whether related or unrelated to those entities specifically identified.

Where numerical ranges are mentioned herein, the invention includesembodiments in which the endpoints are included, embodiments in whichboth endpoints are excluded, and embodiments in which one endpoint isincluded and the other is excluded. It should be assumed that bothendpoints are included unless indicated otherwise. Furthermore, unlessotherwise indicated or otherwise evident from the context andunderstanding of one of ordinary skill in the art.

In the event that any patents, patent applications, or other referencesare incorporated by reference herein and (1) define a term in a mannerthat is inconsistent with and/or (2) are otherwise inconsistent with,either the non-incorporated portion of the present disclosure or any ofthe other incorporated references, the non-incorporated portion of thepresent disclosure shall control, and the term or incorporateddisclosure therein shall only control with respect to the reference inwhich the term is defined and/or the incorporated disclosure was presentoriginally.

What is claimed:
 1. A system for analyzing a sample, comprising: asample card; a planar-area-light source; and an imager comprising animage sensor and a lens, wherein the sample card comprises: a firstplate and a second plate that sandwich a sample, between the two plates,into a thin layer of a thickness of 200 um or less, and wherein thesample contains or is suspected of containing an analyte; wherein theplanar-area-light source comprises: (i) a light extraction plate havinga surface comprising a light scattering structure; and (ii) aside-emitting optical fiber comprising a light emitting sidewalk;wherein the side-emitting optical fiber extends laterally across thelight extraction plate, a portion of the light emitting sidewall ispositioned within the light extraction plate and is configured to emitlight into the light extraction plate; wherein the light scatteringstructure extracts light from inside of the light extraction plate tooutside of the light extraction plate; wherein the sample card ispositioned in parallel with the light extraction plate, such that thelight emitted from the light extraction plate uniformly illuminates asurface area of the sample card; and wherein the imager images thesample.
 2. The system of claim 1, further comprising a light source thatemits light into the side-emitting fiber.
 3. The system of claim 1,wherein the side-emitting optical fiber comprises a material selectedfrom the group consisting of a polymer, an inorganic dielectricmaterial, and silica glass.
 4. The system of claim 1, wherein theside-emitting optical fiber comprises a transmission of 0.5-5% at theinterface between a core and a cladding layer of the optical fiber. 5.The system of claim 1, wherein the diameter of the side-emitting opticalfiber is coextensive with the smallest dimension of the light extractionplate.
 6. The system of claim 1, wherein the length of the side-emittingoptical fiber is 10 mm, 50 mm, 100 mm, 200 mm, 500 mm, or any valuetherebetween.
 7. The system of claim 1, wherein the diameter of theside-emitting optical fiber is 1.5 mm.
 8. The system of claim 1, whereinthe diameter of the side-emitting optical fiber is 1 um, 10 um, 100 um,1 mm, or any value therebetween.
 9. The system of claim 1, wherein thelight extraction plate includes a thickness of 500 um, 1 mm, 2 mm, 4 mm,5 mm, 10 mm, or any value therebetween.
 10. The system of claim 1,wherein the light extraction plate includes has a thickness of 2 mm. 11.The system of claim 1, wherein the light extraction plate includes asurface dimension of 12 mm by 36 mm.
 12. The system of claim 1, whereinthe light extraction plate includes a surface area of 1 cm{circumflexover ( )}2, 10 cm{circumflex over ( )}2, 100 cm{circumflex over ( )}2,or any value therebetween.
 13. The system of claim 1, wherein the lightextraction plate comprises a transparent panel.
 14. The system of claim1, wherein the light extraction plate includes a material selected fromthe group consisting of acrylic, glass, and plastic polymer.
 15. Thesystem of claim 1, wherein the light extraction plate is configured toextract the light traveling therein from at least one of its surfaces.16. The system of claim 1, the light diffuser film is selected from thegroup consisting of opaque white plastic, ground glass, and texturedplastic film.
 17. The system of claim 1, the light diffuser film is incontact with the light extraction plate.
 18. The system of claim 1,wherein the light diffuser film is adhered to the surface of the lightextraction plate.
 19. The system of claim 1, wherein the distancebetween the diffuser film and the light extraction plate is 100 um, 1mm, 2 mm, 5 mm, 10 mm, or any value therebetween.
 20. The system ofclaim 1, wherein the light scattering structure is a structure selectedfrom the group consisting of line arrays, dot arrays, and microlensarrays.
 21. The system of claim 1, wherein the light scatteringstructure is etched, imprinted, printed, or any combination thereof. 22.The system of claim 1, wherein the light scattering structure comprisesparticulates scattered throughout the light extraction plate.
 23. Thesystem of claim 22, wherein the particulates comprise any structurehaving a different reflective index than the light extraction plate. 24.The system of claim 22, wherein the particulates are selected from thegroup consisting of air bubbles, vacuum sealed areas, plastics, andpolymers.
 25. The system of claim 1, wherein the light scatteringstructure is selected from the group consisting of random texturedsurfaces, periodic gratings, painted white dots, microparticles, andnanoparticles.
 26. The system of claim 1, wherein the light source isselected from the group consisting of LED, laser, and incandescent lightbulb.
 27. The system of claim 1, wherein the distance between the samplecard and the planar light extraction plate is less than 5 mm.
 28. Thesystem of claim 1, wherein the sample card is positioned between theimager and the light extraction plate.
 29. The system of claim 1,wherein the first end and the second end of the side-emitting opticalfiber face a light source to receive light.
 30. The system of claim 1,wherein a light diffuser film disposed above the light scatteringstructure.
 31. The system of claim 1, wherein the imaging is formeasuring hemoglobin of the sample.
 32. The system of claim 1, whereinthe extracted light passes through the light diffuser film, therebyproviding a uniform light distribution over a surface area of the lightextraction plate.
 33. The system of claim 1, wherein the side-emittingoptical fiber has two portions inside of the light extraction plate,wherein the distance between the first portion and the second portion islarger than the lateral dimension of a field of view of the imager. 34.The system of claim 33, wherein the distance between the first portionand the second portion is in a range of 5 mm to 50 mm.
 35. The system ofclaim 1, wherein the system further comprises a diffuser film next tothe light extraction plate, and wherein the distance between thediffuser film and the light extraction plate is 100 um, 1 mm, 2 mm, 5mm, or any value therebetween.
 36. The system of claim 1, wherein one orboth of the plates of the sample card comprises spacers, wherein thefirst plate and the second plate are movable from each other intodifferent configurations, including an open configuration and a closedconfiguration; wherein the open configuration is the configuration inwhich the two plates are either partially or completely separated apartand the spacing between the plates is not regulated by the spacers;Wherein the closed configuration is the configuration in which theplates are facing each other, the spacers and a relevant volume of thesample are between the plates, and the spacing between the plates, andthus the thickness of the relevant volume of the sample, is regulated bythe plates and the spacers.
 37. The system of claim 36, wherein thespacers are periodic.
 38. The system of claim 1, wherein the spacershave inter-spacer-distance of 200 um or less.
 39. The system of claim 1,wherein the imaging uses a machine learning model.
 40. The system ofclaim 1, wherein the system further comprises a processor that analyzesthe sample by analyzing the images.
 41. The system of claim 1, whereinthe system further comprises an optical adaptor comprising: a receptacleslot which receives and positions the sample card in the field of viewand focal range of the camera.